Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:43 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the msa package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msa.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1191/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
msa 1.24.0 (landing page) Ulrich Bodenhofer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: msa |
Version: 1.24.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msa_1.24.0.tar.gz |
StartedAt: 2021-10-14 21:25:02 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:27:18 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 136.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: msa.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msa_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/msa.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘msa/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘msa’ version ‘1.24.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘msa’ can be installed ... WARNING Found the following significant warnings: dyn_load.c:1389:37: warning: incompatible pointer types passing 'void (const struct mach_header_64 *, intptr_t)' (aka 'void (const struct mach_header_64 *, long)') to parameter of type 'void (*)(const struct mach_header *, intptr_t)' (aka 'void (*)(const struct mach_header *, long)') [-Wincompatible-pointer-types] dyn_load.c:1390:40: warning: incompatible pointer types passing 'void (const struct mach_header_64 *, intptr_t)' (aka 'void (const struct mach_header_64 *, long)') to parameter of type 'void (*)(const struct mach_header *, intptr_t)' (aka 'void (*)(const struct mach_header *, long)') [-Wincompatible-pointer-types] dyn_load.c:1413:12: warning: '_dyld_bind_fully_image_containing_address' is deprecated: first deprecated in macOS 10.5 - dlopen(RTLD_NOW) [-Wdeprecated-declarations] fileInput/FileParser.cpp:56:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] fileInput/FileParser.cpp:57:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] tree/NJTree.cpp:164:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] multipleAlign/Iteration.cpp:231:17: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] general/UserParameters.cpp:475:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] general/Utility.cpp:53:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] general/ClustalWResources.cpp:106:5: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds] alignment/Alignment.cpp:47:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] alignment/Alignment.cpp:122:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] alignment/Alignment.cpp:617:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] See ‘/Users/biocbuild/bbs-3.13-bioc/meat/msa.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/msa/libs/msa.so’: Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++) Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++) Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_putchar’, possibly from ‘putchar’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed msaPrettyPrint 5.575 0.183 5.787 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/msa.Rcheck/00check.log’ for details.
msa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘msa’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -Wall -g -O2 -c R_init_msa.cpp -o R_init_msa.o In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: ./Muscle/muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: In file included from ./Muscle/muscle.h:38: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -Wall -g -O2 -c SplitCharVector2List.cpp -o SplitCharVector2List.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -Wall -g -O2 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o make --file=msaMakefile --directory=gc-7.2 ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic checking build system type... x86_64-apple-darwin18.7.0 checking host system type... x86_64-apple-darwin18.7.0 checking target system type... x86_64-apple-darwin18.7.0 checking GC version numbers... major=7 minor=2 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking dependency style of gcc... gcc3 checking for inline... inline checking for pthread_self in -lpthread... yes configure: WARNING: "Explicit GC_INIT() calls may be required." checking for xlc... no checking whether gcc supports -fno-strict-aliasing... yes checking whether to build shared libraries... yes checking which machine-dependent code should be used... checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin18.7.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.7.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.7.0 dyld checking how to hardcode library paths into programs... immediate checking whether Solaris gcc optimization fix is necessary... no checking sys/dg_sys_info.h usability... no checking sys/dg_sys_info.h presence... no checking for sys/dg_sys_info.h... no checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for ATOMIC_OPS... no checking which libatomic_ops to use... internal checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bdw-gc.pc config.status: creating include/private/config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing default commands === configuring in libatomic_ops (/Users/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2/libatomic_ops) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' 'PKG_CONFIG_PATH=/usr/local/opt/libxml2/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Resources/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/X11/lib/pkgconfig:/usr/local/opt/openssl@1.1/lib/pkgconfig:/usr/local/opt/mysql-client/lib/pkgconfig' --cache-file=/dev/null --srcdir=. checking build system type... x86_64-apple-darwin18.7.0 checking host system type... x86_64-apple-darwin18.7.0 checking target system type... x86_64-apple-darwin18.7.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for ranlib... ranlib checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for ANSI C header files... (cached) yes checking for PIC compiler flag... -fPIC checking whether gcc -fPIC causes __PIC__ definition... yes checking for pthread_self in -lpthread... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating pkgconfig/atomic_ops.pc config.status: creating pkgconfig/atomic_ops-uninstalled.pc config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/atomic_ops/Makefile config.status: creating src/atomic_ops/sysdeps/Makefile config.status: creating tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands config.status: executing default commands make depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c -fno-common -DPIC -o .libs/allchblk.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c -fno-common -DPIC -o allchblk.o >/dev/null 2>&1 depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF $depbase.Tpo -c -o alloc.lo alloc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c -fno-common -DPIC -o .libs/alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c -fno-common -DPIC -o alloc.o >/dev/null 2>&1 depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF $depbase.Tpo -c -o blacklst.lo blacklst.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c -fno-common -DPIC -o .libs/blacklst.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c -fno-common -DPIC -o blacklst.o >/dev/null 2>&1 depbase=`echo checksums.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF $depbase.Tpo -c -o checksums.lo checksums.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c -fno-common -DPIC -o .libs/checksums.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c -fno-common -DPIC -o checksums.o >/dev/null 2>&1 depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF $depbase.Tpo -c -o dbg_mlc.lo dbg_mlc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c -fno-common -DPIC -o .libs/dbg_mlc.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c -fno-common -DPIC -o dbg_mlc.o >/dev/null 2>&1 depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF $depbase.Tpo -c -o dyn_load.lo dyn_load.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c -fno-common -DPIC -o .libs/dyn_load.o dyn_load.c:1389:37: warning: incompatible pointer types passing 'void (const struct mach_header_64 *, intptr_t)' (aka 'void (const struct mach_header_64 *, long)') to parameter of type 'void (*)(const struct mach_header *, intptr_t)' (aka 'void (*)(const struct mach_header *, long)') [-Wincompatible-pointer-types] _dyld_register_func_for_add_image(GC_dyld_image_add); ^~~~~~~~~~~~~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/mach-o/dyld.h:61:54: note: passing argument to parameter 'func' here extern void _dyld_register_func_for_add_image(void (*func)(const struct mach_header* mh, intptr_t vmaddr_slide)) __OSX_AVAILABLE_STARTING(__MAC_10_1, __IPHONE_2_0); ^ dyn_load.c:1390:40: warning: incompatible pointer types passing 'void (const struct mach_header_64 *, intptr_t)' (aka 'void (const struct mach_header_64 *, long)') to parameter of type 'void (*)(const struct mach_header *, intptr_t)' (aka 'void (*)(const struct mach_header *, long)') [-Wincompatible-pointer-types] _dyld_register_func_for_remove_image(GC_dyld_image_remove); ^~~~~~~~~~~~~~~~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/mach-o/dyld.h:62:57: note: passing argument to parameter 'func' here extern void _dyld_register_func_for_remove_image(void (*func)(const struct mach_header* mh, intptr_t vmaddr_slide)) __OSX_AVAILABLE_STARTING(__MAC_10_1, __IPHONE_2_0); ^ dyn_load.c:1413:12: warning: '_dyld_bind_fully_image_containing_address' is deprecated: first deprecated in macOS 10.5 - dlopen(RTLD_NOW) [-Wdeprecated-declarations] if (!_dyld_bind_fully_image_containing_address( ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/mach-o/dyld.h:244:13: note: '_dyld_bind_fully_image_containing_address' has been explicitly marked deprecated here extern bool _dyld_bind_fully_image_containing_address(const void* address) __API_UNAVAILABLE(ios, tvos, watchos) __OSX_DEPRECATED(10.1, 10.5, "dlopen(RTLD_NOW)"); ^ 3 warnings generated. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c -fno-common -DPIC -o dyn_load.o >/dev/null 2>&1 depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF $depbase.Tpo -c -o finalize.lo finalize.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c -fno-common -DPIC -o .libs/finalize.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c -fno-common -DPIC -o finalize.o >/dev/null 2>&1 depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF $depbase.Tpo -c -o gc_dlopen.lo gc_dlopen.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c -fno-common -DPIC -o .libs/gc_dlopen.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c -fno-common -DPIC -o gc_dlopen.o >/dev/null 2>&1 depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF $depbase.Tpo -c -o gcj_mlc.lo gcj_mlc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c -fno-common -DPIC -o .libs/gcj_mlc.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c -fno-common -DPIC -o gcj_mlc.o >/dev/null 2>&1 depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF $depbase.Tpo -c -o headers.lo headers.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c -fno-common -DPIC -o .libs/headers.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c -fno-common -DPIC -o headers.o >/dev/null 2>&1 depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF $depbase.Tpo -c -o malloc.lo malloc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c -fno-common -DPIC -o .libs/malloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c -fno-common -DPIC -o malloc.o >/dev/null 2>&1 depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF $depbase.Tpo -c -o mallocx.lo mallocx.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c -fno-common -DPIC -o .libs/mallocx.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c -fno-common -DPIC -o mallocx.o >/dev/null 2>&1 depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF $depbase.Tpo -c -o mark.lo mark.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c -fno-common -DPIC -o .libs/mark.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c -fno-common -DPIC -o mark.o >/dev/null 2>&1 depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF $depbase.Tpo -c -o mark_rts.lo mark_rts.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c -fno-common -DPIC -o .libs/mark_rts.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c -fno-common -DPIC -o mark_rts.o >/dev/null 2>&1 depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF $depbase.Tpo -c -o misc.lo misc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c -fno-common -DPIC -o .libs/misc.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c -fno-common -DPIC -o misc.o >/dev/null 2>&1 depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF $depbase.Tpo -c -o new_hblk.lo new_hblk.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c -fno-common -DPIC -o .libs/new_hblk.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c -fno-common -DPIC -o new_hblk.o >/dev/null 2>&1 depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF $depbase.Tpo -c -o obj_map.lo obj_map.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c -fno-common -DPIC -o .libs/obj_map.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c -fno-common -DPIC -o obj_map.o >/dev/null 2>&1 depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF $depbase.Tpo -c -o os_dep.lo os_dep.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c -fno-common -DPIC -o .libs/os_dep.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c -fno-common -DPIC -o os_dep.o >/dev/null 2>&1 depbase=`echo pcr_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF $depbase.Tpo -c -o pcr_interface.lo pcr_interface.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c -fno-common -DPIC -o .libs/pcr_interface.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c -fno-common -DPIC -o pcr_interface.o >/dev/null 2>&1 depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF $depbase.Tpo -c -o ptr_chck.lo ptr_chck.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c -fno-common -DPIC -o .libs/ptr_chck.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c -fno-common -DPIC -o ptr_chck.o >/dev/null 2>&1 depbase=`echo real_malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF $depbase.Tpo -c -o real_malloc.lo real_malloc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c -fno-common -DPIC -o .libs/real_malloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c -fno-common -DPIC -o real_malloc.o >/dev/null 2>&1 depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF $depbase.Tpo -c -o reclaim.lo reclaim.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c -fno-common -DPIC -o .libs/reclaim.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c -fno-common -DPIC -o reclaim.o >/dev/null 2>&1 depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF $depbase.Tpo -c -o specific.lo specific.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c -fno-common -DPIC -o .libs/specific.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c -fno-common -DPIC -o specific.o >/dev/null 2>&1 depbase=`echo stubborn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF $depbase.Tpo -c -o stubborn.lo stubborn.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c -fno-common -DPIC -o .libs/stubborn.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c -fno-common -DPIC -o stubborn.o >/dev/null 2>&1 depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF $depbase.Tpo -c -o typd_mlc.lo typd_mlc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c -fno-common -DPIC -o .libs/typd_mlc.o typd_mlc.c:363:37: warning: shifting a negative signed value is undefined [-Wshift-negative-value] (((word)WORDS_TO_BYTES(-1)) | GC_DS_PER_OBJECT), ^~~~~~~~~~~~~~~~~~ ./include/private/gc_priv.h:565:35: note: expanded from macro 'WORDS_TO_BYTES' # define WORDS_TO_BYTES(x) ((x)<<3) ~~~^ 1 warning generated. libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c -fno-common -DPIC -o typd_mlc.o >/dev/null 2>&1 depbase=`echo backgraph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF $depbase.Tpo -c -o backgraph.lo backgraph.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c -fno-common -DPIC -o .libs/backgraph.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c -fno-common -DPIC -o backgraph.o >/dev/null 2>&1 depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF $depbase.Tpo -c -o thread_local_alloc.lo thread_local_alloc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c -fno-common -DPIC -o .libs/thread_local_alloc.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c -fno-common -DPIC -o thread_local_alloc.o >/dev/null 2>&1 depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF $depbase.Tpo -c -o pthread_start.lo pthread_start.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c -fno-common -DPIC -o .libs/pthread_start.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c -fno-common -DPIC -o pthread_start.o >/dev/null 2>&1 depbase=`echo pthread_support.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF $depbase.Tpo -c -o pthread_support.lo pthread_support.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c -fno-common -DPIC -o .libs/pthread_support.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c -fno-common -DPIC -o pthread_support.o >/dev/null 2>&1 depbase=`echo pthread_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF $depbase.Tpo -c -o pthread_stop_world.lo pthread_stop_world.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c -fno-common -DPIC -o .libs/pthread_stop_world.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c -fno-common -DPIC -o pthread_stop_world.o >/dev/null 2>&1 depbase=`echo darwin_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT darwin_stop_world.lo -MD -MP -MF $depbase.Tpo -c -o darwin_stop_world.lo darwin_stop_world.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT darwin_stop_world.lo -MD -MP -MF .deps/darwin_stop_world.Tpo -c darwin_stop_world.c -fno-common -DPIC -o .libs/darwin_stop_world.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT darwin_stop_world.lo -MD -MP -MF .deps/darwin_stop_world.Tpo -c darwin_stop_world.c -fno-common -DPIC -o darwin_stop_world.o >/dev/null 2>&1 depbase=`echo libatomic_ops/src/atomic_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF $depbase.Tpo -c -o libatomic_ops/src/atomic_ops.lo libatomic_ops/src/atomic_ops.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c -fno-common -DPIC -o libatomic_ops/src/.libs/atomic_ops.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c -fno-common -DPIC -o libatomic_ops/src/atomic_ops.o >/dev/null 2>&1 depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF $depbase.Tpo -c -o mach_dep.lo mach_dep.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c -fno-common -DPIC -o .libs/mach_dep.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c -fno-common -DPIC -o mach_dep.o >/dev/null 2>&1 /bin/sh ./libtool --tag=CC --mode=link gcc -fexceptions -g -O2 -fno-strict-aliasing -Wl,-single_module -version-info 1:3:0 -no-undefined -o libgc.la -rpath /usr/local/lib allchblk.lo alloc.lo blacklst.lo checksums.lo dbg_mlc.lo dyn_load.lo finalize.lo gc_dlopen.lo gcj_mlc.lo headers.lo malloc.lo mallocx.lo mark.lo mark_rts.lo misc.lo new_hblk.lo obj_map.lo os_dep.lo pcr_interface.lo ptr_chck.lo real_malloc.lo reclaim.lo specific.lo stubborn.lo typd_mlc.lo backgraph.lo thread_local_alloc.lo pthread_start.lo pthread_support.lo pthread_stop_world.lo darwin_stop_world.lo libatomic_ops/src/atomic_ops.lo mach_dep.lo -lpthread libtool: link: gcc -dynamiclib -o .libs/libgc.1.dylib .libs/allchblk.o .libs/alloc.o .libs/blacklst.o .libs/checksums.o .libs/dbg_mlc.o .libs/dyn_load.o .libs/finalize.o .libs/gc_dlopen.o .libs/gcj_mlc.o .libs/headers.o .libs/malloc.o .libs/mallocx.o .libs/mark.o .libs/mark_rts.o .libs/misc.o .libs/new_hblk.o .libs/obj_map.o .libs/os_dep.o .libs/pcr_interface.o .libs/ptr_chck.o .libs/real_malloc.o .libs/reclaim.o .libs/specific.o .libs/stubborn.o .libs/typd_mlc.o .libs/backgraph.o .libs/thread_local_alloc.o .libs/pthread_start.o .libs/pthread_support.o .libs/pthread_stop_world.o .libs/darwin_stop_world.o libatomic_ops/src/.libs/atomic_ops.o .libs/mach_dep.o -lpthread -g -O2 -Wl,-single_module -install_name /usr/local/lib/libgc.1.dylib -compatibility_version 2 -current_version 2.3 -Wl,-single_module libtool: link: (cd ".libs" && rm -f "libgc.dylib" && ln -s "libgc.1.dylib" "libgc.dylib") libtool: link: ar cru .libs/libgc.a allchblk.o alloc.o blacklst.o checksums.o dbg_mlc.o dyn_load.o finalize.o gc_dlopen.o gcj_mlc.o headers.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pcr_interface.o ptr_chck.o real_malloc.o reclaim.o specific.o stubborn.o typd_mlc.o backgraph.o thread_local_alloc.o pthread_start.o pthread_support.o pthread_stop_world.o darwin_stop_world.o libatomic_ops/src/atomic_ops.o mach_dep.o /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(checksums.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pcr_interface.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(real_malloc.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(specific.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(backgraph.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pthread_stop_world.o) has no symbols libtool: link: ranlib .libs/libgc.a /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(checksums.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pcr_interface.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(real_malloc.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(specific.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(backgraph.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pthread_stop_world.o) has no symbols libtool: link: ( cd ".libs" && rm -f "libgc.la" && ln -s "../libgc.la" "libgc.la" ) depbase=`echo gc_cpp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF $depbase.Tpo -c -o gc_cpp.lo gc_cpp.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc -fno-common -DPIC -o .libs/gc_cpp.o gc_cpp.cc:37:7: warning: 'operator new' is missing exception specification 'throw(std::bad_alloc)' [-Wmissing-exception-spec] void* operator new( size_t size ) { ^ throw(std::bad_alloc) gc_cpp.cc:41:8: warning: 'operator delete' is missing exception specification 'throw()' [-Wmissing-exception-spec] void operator delete( void* obj ) { ^ throw() gc_cpp.cc:48:7: warning: 'operator new[]' is missing exception specification 'throw(std::bad_alloc)' [-Wmissing-exception-spec] void* operator new[]( size_t size ) { ^ throw(std::bad_alloc) gc_cpp.cc:51:6: warning: 'operator delete[]' is missing exception specification 'throw()' [-Wmissing-exception-spec] void operator delete[]( void* obj ) { ^ throw() 4 warnings generated. libtool: compile: g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc -fno-common -DPIC -o gc_cpp.o >/dev/null 2>&1 /bin/sh ./libtool --tag=CXX --mode=link g++ -fexceptions -g -O2 -version-info 1:3:0 -no-undefined -o libgccpp.la -rpath /usr/local/lib gc_cpp.lo ./libgc.la libtool: link: g++ -dynamiclib -o .libs/libgccpp.1.dylib .libs/gc_cpp.o ./.libs/libgc.dylib -lpthread -g -O2 -install_name /usr/local/lib/libgccpp.1.dylib -compatibility_version 2 -current_version 2.3 -Wl,-single_module libtool: link: (cd ".libs" && rm -f "libgccpp.dylib" && ln -s "libgccpp.1.dylib" "libgccpp.dylib") libtool: link: ar cru .libs/libgccpp.a gc_cpp.o libtool: link: ranlib .libs/libgccpp.a libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" ) depbase=`echo cord/cordbscs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordbscs.lo cord/cordbscs.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c -fno-common -DPIC -o cord/.libs/cordbscs.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c -fno-common -DPIC -o cord/cordbscs.o >/dev/null 2>&1 depbase=`echo cord/cordprnt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordprnt.lo cord/cordprnt.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c -fno-common -DPIC -o cord/.libs/cordprnt.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c -fno-common -DPIC -o cord/cordprnt.o >/dev/null 2>&1 depbase=`echo cord/cordtest.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordtest.lo cord/cordtest.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c -fno-common -DPIC -o cord/.libs/cordtest.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c -fno-common -DPIC -o cord/cordtest.o >/dev/null 2>&1 depbase=`echo cord/cordxtra.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordxtra.lo cord/cordxtra.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF cord/.deps/cordxtra.Tpo -c cord/cordxtra.c -fno-common -DPIC -o cord/.libs/cordxtra.o libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF cord/.deps/cordxtra.Tpo -c cord/cordxtra.c -fno-common -DPIC -o cord/cordxtra.o >/dev/null 2>&1 /bin/sh ./libtool --tag=CC --mode=link gcc -fexceptions -g -O2 -fno-strict-aliasing -version-info 1:3:0 -no-undefined -o libcord.la -rpath /usr/local/lib cord/cordbscs.lo cord/cordprnt.lo cord/cordtest.lo cord/cordxtra.lo ./libgc.la libtool: link: gcc -dynamiclib -o .libs/libcord.1.dylib cord/.libs/cordbscs.o cord/.libs/cordprnt.o cord/.libs/cordtest.o cord/.libs/cordxtra.o ./.libs/libgc.dylib -lpthread -g -O2 -install_name /usr/local/lib/libcord.1.dylib -compatibility_version 2 -current_version 2.3 -Wl,-single_module libtool: link: (cd ".libs" && rm -f "libcord.dylib" && ln -s "libcord.1.dylib" "libcord.dylib") libtool: link: ar cru .libs/libcord.a cord/cordbscs.o cord/cordprnt.o cord/cordtest.o cord/cordxtra.o libtool: link: ranlib .libs/libcord.a libtool: link: ( cd ".libs" && rm -f "libcord.la" && ln -s "../libcord.la" "libcord.la" ) cp .libs/libgc.a ../ cp .libs/libgccpp.a ../ ---------------------------------------- ------------------ GC ----------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=Muscle export PKG_CXXFLAGS=" -I../gc-7.2/include" /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o libMuscle.so aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c aligngivenpath.cpp -o aligngivenpath.o In file included from aligngivenpath.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from aligngivenpath.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o In file included from aligngivenpathsw.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from aligngivenpathsw.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c aligntwomsas.cpp -o aligntwomsas.o In file included from aligntwomsas.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from aligntwomsas.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c aligntwoprofs.cpp -o aligntwoprofs.o In file included from aligntwoprofs.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from aligntwoprofs.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c aln.cpp -o aln.o In file included from aln.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from aln.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c alpha.cpp -o alpha.o In file included from alpha.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^ alpha.cpp:84:10: note: add missing switch cases switch (Alpha) ^ In file included from alpha.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c anchors.cpp -o anchors.o In file included from anchors.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] unsigned uWindowCenter = uBestColIndex + uWindowLength/2; ^ In file included from anchors.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function] static void FindBestColsGrade(const SCORE Score[], unsigned uCount, ^ anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function] static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[], ^ 5 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bittraceback.cpp -o bittraceback.o In file included from bittraceback.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable] char Bits = TraceBack[uLengthA][uLengthB]; ^ In file included from bittraceback.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function] static const char *BitsToStr(char Bits) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c blosum62.cpp -o blosum62.o In file included from blosum62.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from blosum62.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c blosumla.cpp -o blosumla.o In file included from blosumla.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from blosumla.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable] static float Blosum62LA[20][20] = ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c clust.cpp -o clust.o In file included from clust.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ clust.cpp:167:10: note: add missing switch cases switch (m_JoinStyle) ^ clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^ clust.cpp:295:10: note: add missing switch cases switch (m_CentroidStyle) ^ clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable] const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); ^ clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^ clust.cpp:611:10: note: add missing switch cases switch (m_JoinStyle) ^ In file included from clust.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cluster.cpp -o cluster.o In file included from cluster.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] double dMaxDist = 0.0; ^ In file included from cluster.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function] static inline float Max(float d1, float d2) ^ cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function] static inline float Mean(float d1, float d2) ^ 5 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c clwwt.cpp -o clwwt.o In file included from clwwt.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from clwwt.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c color.cpp -o color.o In file included from color.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +4, -2, +0, -2, -1, -2, +0, -2, -1, -1, -1, -1, -2, -1, -1, -1, +1, +0, +0, -3, -1, -2, -1, // A ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:8:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // B ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:9:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -3, +9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -1, -2, -4, // C ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:10:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // D ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // E ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:13:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -3, -2, -3, -3, +6, -3, -1, +0, -3, +0, +0, -3, -4, -3, -3, -2, -2, -1, +1, -1, +3, -3, // F ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:14:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -1, -3, -1, -2, -3, +6, -2, -4, -2, -4, -3, +0, -2, -2, -2, +0, -2, -3, -2, -1, -3, -2, // G ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:15:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -1, -3, -1, +0, -1, -2, +8, -3, -1, -3, -2, +1, -2, +0, +0, -1, -2, -3, -2, -1, +2, +0, // H ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:16:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -3, -1, -3, -3, +0, -4, -3, +4, -3, +2, +1, -3, -3, -3, -3, -2, -1, +3, -3, -1, -1, -3, // I ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:17:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -3, -1, +1, -3, -2, -1, -3, +5, -2, -1, +0, -1, +1, +2, +0, -1, -2, -3, -1, -2, +1, // K ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -4, -1, -4, -3, +0, -4, -3, +2, -2, +4, +2, -3, -3, -2, -2, -2, -1, +1, -2, -1, -1, -3, // L ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -3, -1, -3, -2, +0, -3, -2, +1, -1, +2, +5, -2, -2, +0, -1, -1, -1, +1, -1, -1, -1, -2, // M ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +1, -3, +1, +0, -3, +0, +1, -3, +0, -3, -2, +6, -2, +0, +0, +1, +0, -3, -4, -1, -2, +0, // N ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, +7, -1, -2, -1, -1, -2, -4, -1, -3, -1, // P ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +0, -3, +0, +2, -3, -2, +0, -3, +1, -2, +0, +0, -1, +5, +1, +0, -1, -2, -2, -1, -1, +2, // Q ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -2, -3, -2, +0, -3, -2, +0, -3, +2, -2, -1, +0, -2, +1, +5, -1, -1, -3, -3, -1, -2, +0, // R ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +1, +0, -1, +0, +0, -2, +0, -1, -2, +0, -2, -1, +1, -1, +0, -1, +4, +1, -2, -3, -1, -2, +0, // S ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, +0, -1, -1, -1, +1, +5, +0, -2, -1, -2, -1, // T ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -3, -1, -3, -2, -1, -3, -3, +3, -2, +1, +1, -3, -2, -2, -3, -2, +0, +4, -3, -1, -1, -2, // V ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -3, -4, -2, -4, -3, +1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3,+11, -1, +2, -3, // W ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, // X ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -3, -2, -3, -2, +3, -3, +2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, +2, -1, +7, -2, // Y ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // Z ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from color.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function] static int BlosumScore(char c1, char c2) ^ 26 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cons.cpp -o cons.o In file included from cons.cpp:7: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from cons.cpp:7: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c diaglist.cpp -o diaglist.o In file included from diaglist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from diaglist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c diffobjscore.cpp -o diffobjscore.o In file included from diffobjscore.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] const unsigned uColCount = msa.GetColCount(); ^ In file included from diffobjscore.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c diffpaths.cpp -o diffpaths.o In file included from diffpaths.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from diffpaths.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c difftrees.cpp -o difftrees.o In file included from difftrees.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] const unsigned uLeafCount2 = Tree2.GetLeafCount(); ^ In file included from difftrees.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c difftreese.cpp -o difftreese.o In file included from difftreese.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from difftreese.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c distcalc.cpp -o distcalc.o In file included from distcalc.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from distcalc.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c distfunc.cpp -o distfunc.o In file included from distfunc.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from distfunc.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c distpwkimura.cpp -o distpwkimura.o In file included from distpwkimura.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from distpwkimura.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c domuscle.cpp -o domuscle.o In file included from domuscle.cpp:1: In file included from ./RMuscle.h:4: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable] int PNlength = (msaInput->inputSeqs).Length(); ^ In file included from domuscle.cpp:1: In file included from ./RMuscle.h:4: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dosp.cpp -o dosp.o In file included from dosp.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from dosp.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dpreglist.cpp -o dpreglist.o In file included from dpreglist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1; ^ In file included from dpreglist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c drawtree.cpp -o drawtree.o In file included from drawtree.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from drawtree.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c edgelist.cpp -o edgelist.o In file included from edgelist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from edgelist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c enumopts.cpp -o enumopts.o In file included from enumopts.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from enumopts.cpp:8: ./enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, Amino) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:33:1: note: expanded from here "Amino" ^ In file included from enumopts.cpp:8: ./enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, DNA) ^~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:36:1: note: expanded from here "DNA" ^ In file included from enumopts.cpp:8: ./enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, RNA) ^~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:39:1: note: expanded from here "RNA" ^ In file included from enumopts.cpp:8: ./enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ALPHA) ^~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:18:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Protein) ^~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:43:1: note: expanded from here "Protein" ^ In file included from enumopts.cpp:8: ./enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, DNA) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:46:1: note: expanded from here "DNA" ^ In file included from enumopts.cpp:8: ./enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, RNA) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:49:1: note: expanded from here "RNA" ^ In file included from enumopts.cpp:8: ./enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Auto) ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:52:1: note: expanded from here "Auto" ^ In file included from enumopts.cpp:8: ./enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQTYPE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:25:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, Pseudo) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:56:1: note: expanded from here "Pseudo" ^ In file included from enumopts.cpp:8: ./enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MidLongestSpan) ^~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:59:1: note: expanded from here "MidLongestSpan" ^ In file included from enumopts.cpp:8: ./enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MinAvgLeafDist) ^~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:62:1: note: expanded from here "MinAvgLeafDist" ^ In file included from enumopts.cpp:8: ./enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ROOT) ^~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:31:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMA) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:66:1: note: expanded from here "UPGMA" ^ In file included from enumopts.cpp:8: ./enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMax) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:69:1: note: expanded from here "UPGMAMax" ^ In file included from enumopts.cpp:8: ./enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMin) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:72:1: note: expanded from here "UPGMAMin" ^ In file included from enumopts.cpp:8: ./enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMB) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:75:1: note: expanded from here "UPGMB" ^ In file included from enumopts.cpp:8: ./enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:78:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(CLUSTER) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:39:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NearestNeighbor) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:82:1: note: expanded from here "NearestNeighbor" ^ In file included from enumopts.cpp:8: ./enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:85:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(JOIN) ^~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:44:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Min) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:89:1: note: expanded from here "Min" ^ In file included from enumopts.cpp:8: ./enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Avg) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:92:1: note: expanded from here "Avg" ^ In file included from enumopts.cpp:8: ./enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Max) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:95:1: note: expanded from here "Max" ^ In file included from enumopts.cpp:8: ./enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:98:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Biased) ^~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:101:1: note: expanded from here "Biased" ^ In file included from enumopts.cpp:8: ./enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(LINKAGE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:52:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer6_6) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:105:1: note: expanded from here "Kmer6_6" ^ In file included from enumopts.cpp:8: ./enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_3) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:108:1: note: expanded from here "Kmer20_3" ^ In file included from enumopts.cpp:8: ./enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_4) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:111:1: note: expanded from here "Kmer20_4" ^ In file included from enumopts.cpp:8: ./enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kbit20_3) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:114:1: note: expanded from here "Kbit20_3" ^ In file included from enumopts.cpp:8: ./enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer4_6) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:117:1: note: expanded from here "Kmer4_6" ^ In file included from enumopts.cpp:8: ./enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdKimura) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:120:1: note: expanded from here "PctIdKimura" ^ In file included from enumopts.cpp:8: ./enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdLog) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:123:1: note: expanded from here "PctIdLog" ^ In file included from enumopts.cpp:8: ./enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWKimura) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:126:1: note: expanded from here "PWKimura" ^ In file included from enumopts.cpp:8: ./enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWScoreDist) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:129:1: note: expanded from here "PWScoreDist" ^ In file included from enumopts.cpp:8: ./enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, ScoreDist) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:132:1: note: expanded from here "ScoreDist" ^ In file included from enumopts.cpp:8: ./enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Edit) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:135:1: note: expanded from here "Edit" ^ In file included from enumopts.cpp:8: ./enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(DISTANCE) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:66:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, LE) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:139:1: note: expanded from here "LE" ^ In file included from enumopts.cpp:8: ./enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SP) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:142:1: note: expanded from here "SP" ^ In file included from enumopts.cpp:8: ./enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SV) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:145:1: note: expanded from here "SV" ^ In file included from enumopts.cpp:8: ./enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SPN) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:148:1: note: expanded from here "SPN" ^ In file included from enumopts.cpp:8: ./enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(PPSCORE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:73:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, None) ^~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:152:1: note: expanded from here "None" ^ In file included from enumopts.cpp:8: ./enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, Henikoff) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:155:1: note: expanded from here "Henikoff" ^ In file included from enumopts.cpp:8: ./enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, HenikoffPB) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:158:1: note: expanded from here "HenikoffPB" ^ In file included from enumopts.cpp:8: ./enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, GSC) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:161:1: note: expanded from here "GSC" ^ In file included from enumopts.cpp:8: ./enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ClustalW) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:164:1: note: expanded from here "ClustalW" ^ In file included from enumopts.cpp:8: ./enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ThreeWay) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:167:1: note: expanded from here "ThreeWay" ^ In file included from enumopts.cpp:8: ./enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQWEIGHT) ^~~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:82:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SP) // Sum of Pairs of sequences ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:171:1: note: expanded from here "SP" ^ In file included from enumopts.cpp:8: ./enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, DP) // Dynamic Programming score ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:174:1: note: expanded from here "DP" ^ In file included from enumopts.cpp:8: ./enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:177:1: note: expanded from here "XP" ^ In file included from enumopts.cpp:8: ./enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, PS) // sum of Prof-Seq score for all seqs in MSA ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:180:1: note: expanded from here "PS" ^ In file included from enumopts.cpp:8: ./enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPF) // sum of pairs, fast approximation ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:183:1: note: expanded from here "SPF" ^ In file included from enumopts.cpp:8: ./enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:186:1: note: expanded from here "SPM" ^ In file included from enumopts.cpp:8: ./enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(OBJSCORE) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:91:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Full) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:190:1: note: expanded from here "Full" ^ In file included from enumopts.cpp:8: ./enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Half) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:193:1: note: expanded from here "Half" ^ In file included from enumopts.cpp:8: ./enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Ext) ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ <scratch space>:196:1: note: expanded from here "Ext" ^ In file included from enumopts.cpp:8: ./enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(TERMGAPS) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 65 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c enumtostr.cpp -o enumtostr.o In file included from enumtostr.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from enumtostr.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c estring.cpp -o estring.o In file included from estring.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (nB > 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:397:4: note: remove the 'if' if its condition is always true if (nB > 0) ^~~~~~~~~~~ estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nA < 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:395:8: note: remove the 'if' if its condition is always true else if (nA < 0) ^~~~~~~~~~~ estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nB < 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:386:9: note: remove the 'if' if its condition is always true else if (nB < 0) ^~~~~~~~~~~ estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning char cType; ^ = '\0' In file included from estring.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function] static bool CanMultiplyEstrings(const short es1[], const short es2[]) ^ 6 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fasta.cpp -o fasta.o In file included from fasta.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^ fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] unsigned uColCount = uInsane; ^ In file included from fasta.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fasta2.cpp -o fasta2.o In file included from fasta2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fasta2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastclust.cpp -o fastclust.o In file included from fastclust.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastclust.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastdist.cpp -o fastdist.o In file included from fastdist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastdist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastdistjones.cpp -o fastdistjones.o In file included from fastdistjones.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastdistjones.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastdistkbit.cpp -o fastdistkbit.o In file included from fastdistkbit.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastdistkbit.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastdistkmer.cpp -o fastdistkmer.o In file included from fastdistkmer.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable] double KD = KimuraDist(EstimatedPctId); ^ In file included from fastdistkmer.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastdistmafft.cpp -o fastdistmafft.o In file included from fastdistmafft.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from fastdistmafft.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastdistnuc.cpp -o fastdistnuc.o In file included from fastdistnuc.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from fastdistnuc.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable] static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]); ^ fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 5 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fastscorepath2.cpp -o fastscorepath2.o In file included from fastscorepath2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastscorepath2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c finddiags.cpp -o finddiags.o In file included from finddiags.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from finddiags.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c finddiagsn.cpp -o finddiagsn.o In file included from finddiagsn.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from finddiagsn.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalign.cpp -o glbalign.o In file included from glbalign.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalign.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalign352.cpp -o glbalign352.o In file included from glbalign352.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalign352.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbaligndiag.cpp -o glbaligndiag.o In file included from glbaligndiag.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbaligndiag.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalignle.cpp -o glbalignle.o In file included from glbalignle.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignle.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalignsimple.cpp -o glbalignsimple.o In file included from glbalignsimple.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignsimple.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function] static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB, ^ glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalignsp.cpp -o glbalignsp.o In file included from glbalignsp.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignsp.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalignspn.cpp -o glbalignspn.o In file included from glbalignspn.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignspn.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalignss.cpp -o glbalignss.o In file included from glbalignss.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^ glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^ In file included from glbalignss.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function] static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j) ^ 6 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c glbalndimer.cpp -o glbalndimer.o In file included from glbalndimer.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch] switch (g_PPScore) ^ glbalndimer.cpp:123:10: note: add missing switch cases switch (g_PPScore) ^ In file included from glbalndimer.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c globals.cpp -o globals.o In file included from globals.cpp:6: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from globals.cpp:6: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c globalslinux.cpp -o globalslinux.o In file included from globalslinux.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from globalslinux.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c globalsosx.cpp -o globalsosx.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c globalsother.cpp -o globalsother.o In file included from globalsother.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from globalsother.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c globalswin32.cpp -o globalswin32.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c gonnet.cpp -o gonnet.o In file included from gonnet.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from gonnet.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable] static SCORE Gonnet160[20][20] = ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c henikoffweight.cpp -o henikoffweight.o In file included from henikoffweight.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from henikoffweight.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c henikoffweightpb.cpp -o henikoffweightpb.o In file included from henikoffweightpb.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from henikoffweightpb.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c html.cpp -o html.o In file included from html.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from html.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c hydro.cpp -o hydro.o In file included from hydro.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from hydro.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c intmath.cpp -o intmath.o In file included from intmath.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from intmath.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c local.cpp -o local.o In file included from local.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from local.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c main.cpp -o main.o In file included from main.cpp:3: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from main.cpp:3: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c makerootmsa.cpp -o makerootmsa.o In file included from makerootmsa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] const unsigned uSeqLength = s.Length(); ^ makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable] const PWPath &Path = Nodes[uNodeIndex].m_Path; ^ makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] const unsigned uTreeNodeCount = GuideTree.GetNodeCount(); ^ In file included from makerootmsa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function] static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut) ^ 6 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c makerootmsab.cpp -o makerootmsab.o In file included from makerootmsab.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from makerootmsab.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c maketree.cpp -o maketree.o In file included from maketree.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from maketree.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mhack.cpp -o mhack.o In file included from mhack.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from mhack.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c mpam200.cpp -o mpam200.o In file included from mpam200.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from mpam200.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c msa.cpp -o msa.o In file included from msa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from msa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function] static void FmtChar(char c, unsigned uWidth) ^ msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function] static void FmtInt(unsigned u, unsigned uWidth) ^ msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function] static void FmtInt0(unsigned u, unsigned uWidth) ^ msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function] static void FmtPad(unsigned n) ^ 6 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c msa2.cpp -o msa2.o In file included from msa2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^ msa2.cpp:357:10: note: add missing switch cases switch (Method) ^ msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ In file included from msa2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c msadistkimura.cpp -o msadistkimura.o In file included from msadistkimura.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from msadistkimura.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c msf.cpp -o msf.o In file included from msf.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from msf.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function] static const char *strfind(const char *s, const char *t) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c muscle.cpp -o muscle.o In file included from muscle.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from muscle.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c muscleout.cpp -o muscleout.o In file included from muscleout.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from muscleout.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nucmx.cpp -o nucmx.o In file included from nucmx.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nucmx.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwdasimple.cpp -o nwdasimple.o In file included from nwdasimple.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nwdasimple.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwdasimple2.cpp -o nwdasimple2.o In file included from nwdasimple2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nwdasimple2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwdasmall.cpp -o nwdasmall.o In file included from nwdasmall.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nwdasmall.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwrec.cpp -o nwrec.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nwsmall.cpp -o nwsmall.o In file included from nwsmall.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:394:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:412:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:430:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' In file included from nwsmall.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function] static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c) ^ nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function] static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c) ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c objscore.cpp -o objscore.o In file included from objscore.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch] switch (OS) ^ objscore.cpp:31:10: note: add missing switch cases switch (OS) ^ In file included from objscore.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c objscore2.cpp -o objscore2.o In file included from objscore2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^ objscore2.cpp:22:10: note: add missing switch cases switch (g_TermGaps) ^ objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable] bool bGapping1 = false; ^ objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable] bool bGapping2 = false; ^ objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable] SCORE scoreGaps = 0; ^ objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable] const unsigned uColCount2 = msa2.GetColCount(); ^ objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable] const WEIGHT w = w1*w2; ^ In file included from objscore2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c objscoreda.cpp -o objscoreda.o In file included from objscoreda.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from objscoreda.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c onexception.cpp -o onexception.o In file included from onexception.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from onexception.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c options.cpp -o options.o In file included from options.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ options.cpp:18:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "out", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxIters", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxHours", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapAmbig", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Center", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothScoreCeil", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinBestColScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinSmoothScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ObjScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FromWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ToWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SaveWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "WindowOffset", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FirstWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "AnchorSpacing", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Log", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LogA", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxTrees", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SUEFF", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree_NoWarn", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagLength", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagMargin", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagBreak", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Hydro", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HydroFactor", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SeqType", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxMB", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ComputeWeights", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxSubFam", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ScoreFile", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TermGaps", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTAOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWStrictOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTMLOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSFOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYIOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYSOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Matrix", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:81:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:82:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:83:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:89:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LE", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:90:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SP", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:91:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SV", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPN", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Core", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoCore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags1", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags2", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Quiet", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSF", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Verbose", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Anchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoAnchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Refine", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Profile", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PPScore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ClusterOnly", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Brenner", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Dimer", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clw", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clwstrict", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTML", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Version", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Stable", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Group", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTA", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ProfDB", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PAS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYI", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TomHydro", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MakeTree", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from options.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 103 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c outweights.cpp -o outweights.o In file included from outweights.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from outweights.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pam200mafft.cpp -o pam200mafft.o In file included from pam200mafft.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 408, 20, 54, 52, -182, 179, -68, 109, -35, -47, 39, 106, 206, -14, -12, 257, 293, 191, -306, -219, 0, 0, 0, // A ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:10:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 20, 1190, -228, -295, 94, 6, 63, -131, -184, -176, -112, -29, -122, -195, 49, 185, 13, -49, 199, 333, 0, 0, 0, // C ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:11:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 54, -228, 645, 516, -399, 168, 98, -225, 75, -341, -235, 352, -149, 142, -44, 65, 7, -147, -418, -128, 0, 0, 0, // D ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:12:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 52, -295, 516, 630, -460, 145, 45, -225, 195, -307, -222, 186, -121, 299, 54, -10, -36, -130, -366, -285, 0, 0, 0, // E ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:13:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -182, 94, -399, -460, 908, -387, 82, 100, -423, 340, 87, -216, -160, -274, -307, -31, -153, 51, 19, 604, 0, 0, 0, // F ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:14:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 179, 6, 168, 145, -387, 682, -94, -196, -14, -304, -226, 99, -57, -48, 117, 175, 41, -73, -38, -329, 0, 0, 0, // G ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:15:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -68, 63, 98, 45, 82, -94, 786, -185, 164, -72, -132, 258, 86, 388, 277, 55, -15, -197, -181, 488, 0, 0, 0, // H ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:16:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 109, -131, -225, -225, 100, -196, -185, 574, -204, 308, 411, -94, -95, -202, -188, 1, 182, 489, -254, -133, 0, 0, 0, // I ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:17:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -35, -184, 75, 195, -423, -14, 164, -204, 652, -229, -98, 206, -66, 335, 486, 22, 39, -207, -196, -244, 0, 0, 0, // K ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:18:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -47, -176, -341, -307, 340, -304, -72, 308, -229, 611, 389, -203, 73, -66, -150, -49, -21, 259, -46, -9, 0, 0, 0, // L ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:19:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 39, -112, -235, -222, 87, -226, -132, 411, -98, 389, 776, -111, -78, -104, -109, -29, 149, 351, -209, -162, 0, 0, 0, // M ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:20:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 106, -29, 352, 186, -216, 99, 258, -94, 206, -203, -111, 536, -1, 108, 93, 260, 188, -98, -359, 12, 0, 0, 0, // N ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:21:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 206, -122, -149, -121, -160, -57, 86, -95, -66, 73, -78, -1, 756, 142, 25, 241, 159, -55, -353, -206, 0, 0, 0, // P ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:22:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -14, -195, 142, 299, -274, -48, 388, -202, 335, -66, -104, 108, 142, 655, 321, 7, -15, -175, -223, -53, 0, 0, 0, // Q ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:23:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -12, 49, -44, 54, -307, 117, 277, -188, 486, -150, -109, 93, 25, 321, 626, 48, 16, -181, 124, -113, 0, 0, 0, // R ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:24:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 257, 185, 65, -10, -31, 175, 55, 1, 22, -49, -29, 260, 241, 7, 48, 373, 279, 28, -193, -35, 0, 0, 0, // S ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:25:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 293, 13, 7, -36, -153, 41, -15, 182, 39, -21, 149, 188, 159, -15, 16, 279, 442, 163, -323, -170, 0, 0, 0, // T ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:26:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 191, -49, -147, -130, 51, -73, -197, 489, -207, 259, 351, -98, -55, -175, -181, 28, 163, 525, -225, -177, 0, 0, 0, // V ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -306, 199, -418, -366, 19, -38, -181, -254, -196, -46, -209, -359, -353, -223, 124, -193, -323, -225, 1495, 83, 0, 0, 0, // W ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -219, 333, -128, -285, 604, -329, 488, -133, -244, -9, -162, 12, -206, -53, -113, -35, -170, -177, 83, 999, 0, 0, 0, // Y ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:29:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // B ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:30:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // Z ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:31:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // X ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from pam200mafft.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable] static float PAM200[23][23] = ^ 26 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c params.cpp -o params.o In file included from params.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^ params.cpp:441:10: note: add missing switch cases switch (g_PPScore) ^ In file included from params.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c phy.cpp -o phy.o In file included from phy.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] double dEdgeLength = GetEdgeLength(uNode1, uNode2); ^ In file included from phy.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c phy2.cpp -o phy2.o In file included from phy2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phy2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c phy3.cpp -o phy3.o In file included from phy3.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] const double dThisDist = tree.GetEdgeLength(uNode1, uNode2); ^ phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] unsigned uMaxFrom = NULL_NEIGHBOR; ^ phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] double dAllMaxDist = -1e20; ^ phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] const unsigned uLeafCount = tree.GetLeafCount(); ^ phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] unsigned uMaxTo = NULL_NEIGHBOR; ^ In file included from phy3.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function] static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount) ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c phy4.cpp -o phy4.o In file included from phy4.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phy4.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c phyfromclust.cpp -o phyfromclust.o In file included from phyfromclust.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phyfromclust.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c phyfromfile.cpp -o phyfromfile.o In file included from phyfromfile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phyfromfile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c physeq.cpp -o physeq.o In file included from physeq.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from physeq.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c phytofile.cpp -o phytofile.o In file included from phytofile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phytofile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c posgap.cpp -o posgap.o In file included from posgap.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from posgap.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ppscore.cpp -o ppscore.o In file included from ppscore.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from ppscore.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c profdb.cpp -o profdb.o In file included from profdb.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from profdb.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from profdb.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c profile.cpp -o profile.o In file included from profile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from profile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c profilefrommsa.cpp -o profilefrommsa.o In file included from profilefrommsa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^ profilefrommsa.cpp:230:10: note: add missing switch cases switch (g_Alpha) ^ profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] unsigned uHydrophobicRunLength = 0; ^ profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = a.GetSeqCount(); ^ In file included from profilefrommsa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 6 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c progalign.cpp -o progalign.o In file included from progalign.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] const unsigned uIterCount = uSeqCount - 1; ^ In file included from progalign.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c progress.cpp -o progress.o In file included from progress.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from progress.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c progressivealign.cpp -o progressivealign.o In file included from progressivealign.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from progressivealign.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pwpath.cpp -o pwpath.o In file included from pwpath.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable] const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); ^ pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] unsigned uEdgeIndex = 0; ^ In file included from pwpath.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c readmx.cpp -o readmx.o In file included from readmx.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from readmx.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function] static unsigned MxCharToLetter(char c) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c realigndiffs.cpp -o realigndiffs.o In file included from realigndiffs.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from realigndiffs.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c realigndiffse.cpp -o realigndiffse.o In file included from realigndiffse.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable] unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); ^ realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable] unsigned uOldRight = OldTree.GetRight(uOld); ^ In file included from realigndiffse.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c refine.cpp -o refine.o In file included from refine.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refine.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from refine.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c refinehoriz.cpp -o refinehoriz.o In file included from refinehoriz.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ refinehoriz.cpp:260:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ refinehoriz.cpp:263:56: note: uninitialized use occurs here RefineHeightParts(msaIn, tree, Internals, bReverse, bRight, ^~~~~~ refinehoriz.cpp:251:15: note: initialize the variable 'bRight' to silence this warning bool bRight; ^ = false In file included from refinehoriz.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c refinesubfams.cpp -o refinesubfams.o In file included from refinesubfams.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] const unsigned uNodeCount = tree.GetNodeCount(); ^ In file included from refinesubfams.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c refinetree.cpp -o refinetree.o In file included from refinetree.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refinetree.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c refinetreee.cpp -o refinetreee.o In file included from refinetreee.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refinetreee.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c refinevert.cpp -o refinevert.o In file included from refinevert.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refinevert.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c refinew.cpp -o refinew.o In file included from refinew.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable] unsigned uOutCols = msaOut.GetColCount(); ^ In file included from refinew.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c savebest.cpp -o savebest.o In file included from savebest.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from savebest.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scoredist.cpp -o scoredist.o In file included from scoredist.cpp:3: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scoredist.cpp:3: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable] static const double Dayhoff_CalibrationFactor = 1.3370; ^ scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable] static const double MV_CalibrationFactor = 1.1775; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scoregaps.cpp -o scoregaps.o In file included from scoregaps.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scoregaps.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function] static void FreeGapInfo(GAPINFO *GI) ^ scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function] static SCORE Penalty(unsigned Length, bool Term) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scorehistory.cpp -o scorehistory.o In file included from scorehistory.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scorehistory.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scorepp.cpp -o scorepp.o In file included from scorepp.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scorepp.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c seq.cpp -o seq.o In file included from seq.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from seq.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c seqvect.cpp -o seqvect.o In file included from seqvect.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] return (Seq &) *((Seq *) 0); ^~~~~~~~~~~~ In file included from seqvect.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable] const size_t MAX_FASTA_LINE = 16000; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c setblosumweights.cpp -o setblosumweights.o In file included from setblosumweights.cpp:42: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from setblosumweights.cpp:42: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c setgscweights.cpp -o setgscweights.o In file included from setgscweights.cpp:104: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from setgscweights.cpp:104: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c setnewhandler.cpp -o setnewhandler.o In file included from setnewhandler.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from setnewhandler.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c spfast.cpp -o spfast.o In file included from spfast.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ In file included from spfast.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function] static const char *GapTypeToStr(int GapType) ^ spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function] static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) ^ 5 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sptest.cpp -o sptest.o In file included from sptest.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from sptest.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c stabilize.cpp -o stabilize.o In file included from stabilize.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from stabilize.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c subfam.cpp -o subfam.o In file included from subfam.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] int NotUsed = system(CmdLine); ^ In file included from subfam.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c subfams.cpp -o subfams.o In file included from subfams.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from subfams.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ subfams.cpp:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function] static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2) ^ subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function] static void InitializeSingleSource(DistFunc &DF, unsigned uIndex) ^ subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function] static void Relax(DistFunc &DF, unsigned u, unsigned v) ^ 5 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sw.cpp -o sw.o In file included from sw.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from sw.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c termgaps.cpp -o termgaps.o In file included from termgaps.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from termgaps.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c textfile.cpp -o textfile.o In file included from textfile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable] int i = fputc(c, m_ptrFile); ^ textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable] int iError = fputs(szLine, m_ptrFile); ^ In file included from textfile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threewaywt.cpp -o threewaywt.o In file included from threewaywt.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from threewaywt.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tomhydro.cpp -o tomhydro.o In file included from tomhydro.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from tomhydro.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c traceback.cpp -o traceback.o In file included from traceback.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:186:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:150:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:112:9: note: remove the 'if' if its condition is always true else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from traceback.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tracebackopt.cpp -o tracebackopt.o In file included from tracebackopt.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from tracebackopt.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c tracebacksw.cpp -o tracebacksw.o In file included from tracebacksw.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB); ^ tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from tracebacksw.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c treefrommsa.cpp -o treefrommsa.o In file included from treefrommsa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from treefrommsa.cpp:5: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from treefrommsa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c typetostr.cpp -o typetostr.o In file included from typetostr.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from typetostr.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c upgma2.cpp -o upgma2.o In file included from upgma2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ upgma2.cpp:292:17: note: uninitialized use occurs here g_Dist[vL] = dtNewDist; ^~~~~~~~~ upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning dist_t dtNewDist; ^ = 0.0 upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 2, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 2, 0, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 0, 4, 20, ^~~~~~~~~~~~~~~~~~ { } upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 4, 0, 20, ^~~~~~~~~~~~~~~~~~ { } upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 20, 20, 20, 20, 0, ^~~~~~~~~~~~~~~~~~ { } In file included from upgma2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function] static void ListState() ^ 9 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c usage.cpp -o usage.o In file included from usage.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from usage.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c validateids.cpp -o validateids.o In file included from validateids.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from validateids.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c vtml2.cpp -o vtml2.o In file included from vtml2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from vtml2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c writescorefile.cpp -o writescorefile.o In file included from writescorefile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ writescorefile.cpp:40:12: note: uninitialized use occurs here dSum += Score; ^~~~~ writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning double Score; ^ = 0.0 In file included from writescorefile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RMuscle.cpp -o RMuscle.o In file included from RMuscle.cpp:1: In file included from ./RMuscle.h:4: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from RMuscle.cpp:1: In file included from ./RMuscle.h:4: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o libMuscle.so aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ar rcs libMuscle.a aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(blosumla.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(glbalign352.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(globalslinux.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(globalsother.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(globalswin32.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(nwdasimple2.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(nwdasmall.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(nwrec.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(objscoreda.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(pam200mafft.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(validateids.o) has no symbols cp libMuscle.a ../ ---------------------------------------- ---------------- MUSCLE ---------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=ClustalW ./configure; \ cd src; \ export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I. "; \ /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \ ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \ cp libClustalW.a ../../ checking build system type... i386-apple-darwin18.7.0 checking host system type... i386-apple-darwin18.7.0 checking target system type... i386-apple-darwin18.7.0 building for darwin18.7.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o In file included from pairwise/FullPairwiseAlign.cpp:9: In file included from pairwise/FullPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:42: pairwise/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from pairwise/FullPairwiseAlign.cpp:9: In file included from pairwise/FullPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:43: pairwise/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from pairwise/FullPairwiseAlign.cpp:9: In file included from pairwise/FullPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../substitutionMatrix/../general/clustalw.h:44: pairwise/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o In file included from pairwise/FastPairwiseAlign.cpp:10: In file included from pairwise/FastPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:42: pairwise/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from pairwise/FastPairwiseAlign.cpp:10: In file included from pairwise/FastPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:43: pairwise/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from pairwise/FastPairwiseAlign.cpp:10: In file included from pairwise/FastPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../substitutionMatrix/../general/clustalw.h:44: pairwise/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o In file included from fileInput/MSFFileParser.cpp:16: In file included from fileInput/MSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/MSFFileParser.cpp:16: In file included from fileInput/MSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/MSFFileParser.cpp:16: In file included from fileInput/MSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o In file included from fileInput/FileReader.cpp:29: In file included from fileInput/FileReader.h:12: In file included from fileInput/../alignment/Alignment.h:41: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/FileReader.cpp:29: In file included from fileInput/FileReader.h:12: In file included from fileInput/../alignment/Alignment.h:41: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/FileReader.cpp:29: In file included from fileInput/FileReader.h:12: In file included from fileInput/../alignment/Alignment.h:41: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../substitutionMatrix/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o In file included from fileInput/PIRFileParser.cpp:16: In file included from fileInput/PIRFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PIRFileParser.cpp:16: In file included from fileInput/PIRFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PIRFileParser.cpp:16: In file included from fileInput/PIRFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o In file included from fileInput/RSFFileParser.cpp:16: In file included from fileInput/RSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/RSFFileParser.cpp:16: In file included from fileInput/RSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/RSFFileParser.cpp:16: In file included from fileInput/RSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o In file included from fileInput/GDEFileParser.cpp:16: In file included from fileInput/GDEFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/GDEFileParser.cpp:16: In file included from fileInput/GDEFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/GDEFileParser.cpp:16: In file included from fileInput/GDEFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o In file included from fileInput/ClustalFileParser.cpp:19: In file included from fileInput/ClustalFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/ClustalFileParser.cpp:19: In file included from fileInput/ClustalFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/ClustalFileParser.cpp:19: In file included from fileInput/ClustalFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o In file included from fileInput/PearsonFileParser.cpp:26: In file included from fileInput/PearsonFileParser.h:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PearsonFileParser.cpp:26: In file included from fileInput/PearsonFileParser.h:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PearsonFileParser.cpp:26: In file included from fileInput/PearsonFileParser.h:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/FileParser.cpp -o fileInput/FileParser.o In file included from fileInput/FileParser.cpp:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/FileParser.cpp:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable] int n = (*input).inputSeqs.size(); ^ fileInput/FileParser.cpp:56:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ fileInput/FileParser.cpp:57:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char c; ^~~~~~~~~ In file included from fileInput/FileParser.cpp:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 6 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o In file included from fileInput/EMBLFileParser.cpp:16: In file included from fileInput/EMBLFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/EMBLFileParser.cpp:16: In file included from fileInput/EMBLFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/EMBLFileParser.cpp:16: In file included from fileInput/EMBLFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o In file included from tree/UPGMA/RootedClusterTree.cpp:9: In file included from tree/UPGMA/RootedClusterTree.h:8: In file included from tree/UPGMA/../ClusterTree.h:20: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:42: tree/UPGMA/../../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedClusterTree.cpp:9: In file included from tree/UPGMA/RootedClusterTree.h:8: In file included from tree/UPGMA/../ClusterTree.h:20: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:43: tree/UPGMA/../../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedClusterTree.cpp:9: In file included from tree/UPGMA/RootedClusterTree.h:8: In file included from tree/UPGMA/../ClusterTree.h:20: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../general/clustalw.h:44: tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from tree/UPGMA/UPGMAAlgorithm.h:6: In file included from tree/UPGMA/../../general/clustalw.h:42: tree/UPGMA/../../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from tree/UPGMA/UPGMAAlgorithm.h:6: In file included from tree/UPGMA/../../general/clustalw.h:43: tree/UPGMA/../../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from tree/UPGMA/UPGMAAlgorithm.h:6: In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h:44: tree/UPGMA/../../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o In file included from tree/UPGMA/Node.cpp:7: In file included from tree/UPGMA/../../general/clustalw.h:42: tree/UPGMA/../../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/Node.cpp:7: In file included from tree/UPGMA/../../general/clustalw.h:43: tree/UPGMA/../../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/Node.cpp:7: In file included from tree/UPGMA/../../general/clustalw.h:44: tree/UPGMA/../../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o In file included from tree/UPGMA/RootedGuideTree.cpp:10: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:42: tree/UPGMA/../../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedGuideTree.cpp:10: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:43: tree/UPGMA/../../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedGuideTree.cpp:10: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/clustalw.h:44: tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o In file included from tree/UPGMA/RootedTreeOutput.cpp:9: In file included from tree/UPGMA/RootedTreeOutput.h:15: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:42: tree/UPGMA/../../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedTreeOutput.cpp:9: In file included from tree/UPGMA/RootedTreeOutput.h:15: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:43: tree/UPGMA/../../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedTreeOutput.cpp:9: In file included from tree/UPGMA/RootedTreeOutput.h:15: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../general/clustalw.h:44: tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/Tree.cpp -o tree/Tree.o In file included from tree/Tree.cpp:10: In file included from tree/Tree.h:13: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/Tree.cpp:10: In file included from tree/Tree.h:13: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/Tree.cpp:10: In file included from tree/Tree.h:13: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../substitutionMatrix/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o In file included from tree/ClusterTree.cpp:9: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/ClusterTree.cpp:9: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/ClusterTree.cpp:9: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o In file included from tree/TreeInterface.cpp:15: In file included from tree/TreeInterface.h:19: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/TreeInterface.cpp:15: In file included from tree/TreeInterface.h:19: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/TreeInterface.cpp:15: In file included from tree/TreeInterface.h:19: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o In file included from tree/UnRootedClusterTree.cpp:9: In file included from tree/UnRootedClusterTree.h:8: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UnRootedClusterTree.cpp:9: In file included from tree/UnRootedClusterTree.h:8: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UnRootedClusterTree.cpp:9: In file included from tree/UnRootedClusterTree.h:8: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o In file included from tree/ClusterTreeOutput.cpp:9: In file included from tree/ClusterTreeOutput.h:11: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/ClusterTreeOutput.cpp:9: In file included from tree/ClusterTreeOutput.h:11: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/ClusterTreeOutput.cpp:9: In file included from tree/ClusterTreeOutput.h:11: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/NJTree.cpp -o tree/NJTree.o In file included from tree/NJTree.cpp:10: In file included from tree/NJTree.h:11: In file included from tree/ClusterTreeAlgorithm.h:12: In file included from tree/../general/clustalw.h:42: tree/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/NJTree.cpp:10: In file included from tree/NJTree.h:11: In file included from tree/ClusterTreeAlgorithm.h:12: In file included from tree/../general/clustalw.h:43: tree/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ tree/NJTree.cpp:164:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from tree/NJTree.cpp:10: In file included from tree/NJTree.h:11: In file included from tree/ClusterTreeAlgorithm.h:12: In file included from tree/../general/clustalw.h:44: tree/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o In file included from interface/CommandLineParser.cpp:13: In file included from interface/CommandLineParser.h:18: In file included from interface/../Clustal.h:15: In file included from ./general/clustalw.h:42: ./general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from interface/CommandLineParser.cpp:13: In file included from interface/CommandLineParser.h:18: In file included from interface/../Clustal.h:15: In file included from ./general/clustalw.h:43: ./general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from interface/CommandLineParser.cpp:13: In file included from interface/CommandLineParser.h:18: In file included from interface/../Clustal.h:15: In file included from interface/../general/clustalw.h:44: ./general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o In file included from substitutionMatrix/SubMatrix.cpp:15: In file included from substitutionMatrix/SubMatrix.h:28: In file included from substitutionMatrix/../general/clustalw.h:42: substitutionMatrix/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from substitutionMatrix/SubMatrix.cpp:15: In file included from substitutionMatrix/SubMatrix.h:28: In file included from substitutionMatrix/../general/clustalw.h:43: substitutionMatrix/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable] int nmat; ^ substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable] int n, llimit, ulimit; ^ substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable] int n, llimit, ulimit; ^ substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable] int n, llimit, ulimit; ^ substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable] char inline1[1024]; ^ In file included from substitutionMatrix/SubMatrix.cpp:15: In file included from substitutionMatrix/SubMatrix.h:28: In file included from substitutionMatrix/../general/clustalw.h:44: substitutionMatrix/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o In file included from multipleAlign/Iteration.cpp:13: In file included from multipleAlign/Iteration.h:8: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/Iteration.cpp:13: In file included from multipleAlign/Iteration.h:8: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ multipleAlign/Iteration.cpp:231:17: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] tmpnam (buffer); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/stdio.h:186:1: note: 'tmpnam' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/sys/cdefs.h:180:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((deprecated(_msg))) ^ In file included from multipleAlign/Iteration.cpp:13: In file included from multipleAlign/Iteration.h:8: In file included from multipleAlign/../tree/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../tree/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o In file included from multipleAlign/MSA.cpp:16: In file included from multipleAlign/MSA.h:10: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/MSA.cpp:16: In file included from multipleAlign/MSA.h:10: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 ^ In file included from multipleAlign/MSA.cpp:16: In file included from multipleAlign/MSA.h:10: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from multipleAlign/MyersMillerProfileAlign.h:10: In file included from multipleAlign/ProfileAlignAlgorithm.h:10: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from multipleAlign/MyersMillerProfileAlign.h:10: In file included from multipleAlign/ProfileAlignAlgorithm.h:10: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from multipleAlign/MyersMillerProfileAlign.h:10: In file included from multipleAlign/ProfileAlignAlgorithm.h:10: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: multipleAlign/MyersMillerProfileAlign.h:60:13: warning: private field 'matrix' is not used [-Wunused-private-field] int matrix[32][32]; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o In file included from multipleAlign/ProfileStandard.cpp:9: In file included from multipleAlign/ProfileStandard.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileStandard.cpp:9: In file included from multipleAlign/ProfileStandard.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileStandard.cpp:9: In file included from multipleAlign/ProfileStandard.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o In file included from multipleAlign/ProfileWithSub.cpp:9: In file included from multipleAlign/ProfileWithSub.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileWithSub.cpp:9: In file included from multipleAlign/ProfileWithSub.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileWithSub.cpp:9: In file included from multipleAlign/ProfileWithSub.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o In file included from multipleAlign/ProfileBase.cpp:9: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileBase.cpp:9: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileBase.cpp:9: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o In file included from multipleAlign/LowScoreSegProfile.cpp:9: In file included from multipleAlign/LowScoreSegProfile.h:13: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/LowScoreSegProfile.cpp:9: In file included from multipleAlign/LowScoreSegProfile.h:13: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/LowScoreSegProfile.cpp:9: In file included from multipleAlign/LowScoreSegProfile.h:13: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../substitutionMatrix/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/OutputFile.cpp -o general/OutputFile.o In file included from general/OutputFile.cpp:10: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/OutputFile.cpp:10: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/OutputFile.cpp:10: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/UserParameters.cpp -o general/UserParameters.o In file included from general/UserParameters.cpp:24: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/UserParameters.cpp:24: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ general/UserParameters.cpp:475:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ In file included from general/UserParameters.cpp:24: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/Utility.cpp -o general/Utility.o In file included from general/Utility.cpp:19: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/Utility.cpp:19: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ general/Utility.cpp:53:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p; ^~~~~~~~~ In file included from general/Utility.cpp:19: In file included from general/Utility.h:15: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/DebugLog.cpp -o general/DebugLog.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/ClustalWResources.cpp -o general/ClustalWResources.o In file included from general/ClustalWResources.cpp:14: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/ClustalWResources.cpp:14: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ general/ClustalWResources.cpp:106:5: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds] delim[1] = 0; ^ ~ general/ClustalWResources.cpp:104:5: note: array 'delim' declared here char delim[1]; ^ In file included from general/ClustalWResources.cpp:14: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/SymMatrix.cpp -o general/SymMatrix.o In file included from general/SymMatrix.cpp:10: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c general/Stats.cpp -o general/Stats.o In file included from general/Stats.cpp:15: In file included from general/../alignment/Alignment.h:41: In file included from general/../alignment/Sequence.h:20: In file included from general/../alignment/../general/userparams.h:8: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/Stats.cpp:15: In file included from general/../alignment/Alignment.h:41: In file included from general/../alignment/Sequence.h:20: In file included from general/../alignment/../general/userparams.h:8: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/Stats.cpp:15: In file included from general/../alignment/Alignment.h:41: In file included from general/../alignment/Sequence.h:20: In file included from general/../alignment/../substitutionMatrix/../general/userparams.h:8: In file included from general/UserParameters.h:22: In file included from general/../alignment/../substitutionMatrix/../general/utils.h:8: In file included from general/Utility.h:15: In file included from general/../alignment/../substitutionMatrix/../general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c Help.cpp -o Help.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c alignment/Alignment.cpp -o alignment/Alignment.o In file included from alignment/Alignment.cpp:25: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/Alignment.cpp:25: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ alignment/Alignment.cpp:47:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int sl; /* which have code = gap_pos2 */ ^~~~~~~~~ alignment/Alignment.cpp:122:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int sl; /* which have code = gap_pos2 */ ^~~~~~~~~ alignment/Alignment.cpp:617:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int sl; ^~~~~~~~~ alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^ In file included from alignment/Alignment.cpp:25: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../substitutionMatrix/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../substitutionMatrix/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../substitutionMatrix/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o In file included from alignment/AlignmentOutput.cpp:27: In file included from alignment/AlignmentOutput.h:24: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/AlignmentOutput.cpp:27: In file included from alignment/AlignmentOutput.h:24: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/AlignmentOutput.cpp:27: In file included from alignment/AlignmentOutput.h:24: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../substitutionMatrix/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../substitutionMatrix/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../substitutionMatrix/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o In file included from alignment/ObjectiveScore.cpp:10: In file included from alignment/ObjectiveScore.h:14: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/ObjectiveScore.cpp:10: In file included from alignment/ObjectiveScore.h:14: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/ObjectiveScore.cpp:10: In file included from alignment/ObjectiveScore.h:14: In file included from alignment/../substitutionMatrix/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ In file included from alignment/ObjectiveScore.cpp:10: alignment/ObjectiveScore.h:40:14: warning: private field 'scale' is not used [-Wunused-private-field] long scale; ^ alignment/ObjectiveScore.h:41:13: warning: private field 'weightScale' is not used [-Wunused-private-field] int weightScale; ^ alignment/ObjectiveScore.h:42:13: warning: private field 'sagaGapEx' is not used [-Wunused-private-field] int sagaGapEx, sagaGapOp; ^ alignment/ObjectiveScore.h:42:24: warning: private field 'sagaGapOp' is not used [-Wunused-private-field] int sagaGapEx, sagaGapOp; ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c alignment/Sequence.cpp -o alignment/Sequence.o In file included from alignment/Sequence.cpp:10: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/Sequence.cpp:10: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/Sequence.cpp:10: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c Clustal.cpp -o Clustal.o In file included from Clustal.cpp:27: In file included from ./Clustal.h:15: In file included from ./general/clustalw.h:42: ./general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from Clustal.cpp:27: In file included from ./Clustal.h:15: In file included from ./general/clustalw.h:43: ./general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from Clustal.cpp:27: In file included from ./Clustal.h:15: In file included from ./fileInput/../alignment/../general/clustalw.h:44: ./general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c RClustalWMain.cpp -o RClustalWMain.o In file included from RClustalWMain.cpp:5: In file included from ./alignment/Alignment.h:41: In file included from ./alignment/Sequence.h:20: In file included from ./alignment/../general/userparams.h:8: In file included from ./alignment/../general/UserParameters.h:22: In file included from ./alignment/../general/utils.h:8: In file included from ./alignment/../general/Utility.h:15: In file included from ./alignment/../general/clustalw.h:42: ./alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalWMain.cpp:5: In file included from ./alignment/Alignment.h:41: In file included from ./alignment/Sequence.h:20: In file included from ./alignment/../general/userparams.h:8: In file included from ./alignment/../general/UserParameters.h:22: In file included from ./alignment/../general/utils.h:8: In file included from ./alignment/../general/Utility.h:15: In file included from ./alignment/../general/clustalw.h:43: ./alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalWMain.cpp:5: In file included from ./fileInput/../alignment/Alignment.h:41: In file included from ./fileInput/../alignment/Sequence.h:20: In file included from ./interface/../general/userparams.h:8: In file included from ./general/UserParameters.h:22: In file included from ./interface/../general/utils.h:8: In file included from ./general/Utility.h:15: In file included from ./interface/../general/clustalw.h:44: ./alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DHAVE_CONFIG_H -I. -fPIC -Wall -g -O2 -c RClustalW.cpp -o RClustalW.o In file included from RClustalW.cpp:2: In file included from ./RClustalWMain.h:6: In file included from ./general/clustalw.h:42: ./general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalW.cpp:2: In file included from ./RClustalWMain.h:6: In file included from ./general/clustalw.h:43: ./general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalW.cpp:2: In file included from ./RClustalWMain.h:6: In file included from ./general/clustalw.h:44: ./general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o libClustalW.so pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libClustalW.a(InvalidCombination.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libClustalW.a(SymMatrix.o) has no symbols ---------------------------------------- --------------- ClustalW --------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=ClustalOmega ./configure `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \ export PKG_LIBS=" "; \ export PKG_CXXFLAGS=" `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"` -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \ export PKG_CFLAGS=" -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \ cd src; \ /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \ ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \ cp libClustalOmega.a ../../ configure: Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... i386-apple-darwin18.7.0 checking host system type... i386-apple-darwin18.7.0 checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.7.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.7.0 dyld checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... no checking for fseeko64... no checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 8 checking if malloc debugging is wanted... no checking whether to build with debug information... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/exceptions4c/Makefile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/argtable2/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/argtable2.c -o argtable2/argtable2.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/arg_end.c -o argtable2/arg_end.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/arg_rem.c -o argtable2/arg_rem.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/arg_lit.c -o argtable2/arg_lit.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/arg_int.c -o argtable2/arg_int.o argtable2/arg_int.c:60:12: warning: implicitly declaring library function 'isspace' with type 'int (int)' [-Wimplicit-function-declaration] while (isspace(*ptr)) ^ argtable2/arg_int.c:60:12: note: include the header <ctype.h> or explicitly provide a declaration for 'isspace' argtable2/arg_int.c:89:8: warning: implicitly declaring library function 'toupper' with type 'int (int)' [-Wimplicit-function-declaration] if (toupper(*ptr++)!=toupper(X)) ^ argtable2/arg_int.c:89:8: note: include the header <ctype.h> or explicitly provide a declaration for 'toupper' 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/arg_str.c -o argtable2/arg_str.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c argtable2/arg_file.c -o argtable2/arg_file.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c kmpp/KMeans.cpp -o kmpp/KMeans.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c kmpp/KmTree.cpp -o kmpp/KmTree.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o In file included from clustal/hhalign_wrapper.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/hhalign_wrapper.c:85:9: warning: unused variable 'iLen' [-Wunused-variable] int iLen; /* length of sequence */ ^ clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable] int iR; /* iterator for residue */ ^ 3 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o In file included from clustal/ktuple_pair.c:29: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/list.c -o clustal/list.o In file included from clustal/list.c:32: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/log.c -o clustal/log.o In file included from clustal/log.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/muscle_tree.c -o clustal/muscle_tree.o clustal/muscle_tree.c:42:21: warning: unused variable 'VERY_NEGATIVE_DOUBLE' [-Wunused-const-variable] static const double VERY_NEGATIVE_DOUBLE = -9e29; ^ clustal/muscle_tree.c:519:1: warning: unused function 'IsEdge' [-Wunused-function] IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree) ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/mbed.c -o clustal/mbed.o In file included from clustal/mbed.c:28: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/mbed.c:69:18: warning: unused variable 'MAX_ALLOWED_SEQ_PER_PRECLUSTER' [-Wunused-const-variable] static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100; ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/pair_dist.c -o clustal/pair_dist.o In file included from clustal/pair_dist.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable] bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE; ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/progress.c -o clustal/progress.o In file included from clustal/progress.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/seq.c -o clustal/seq.o In file included from clustal/seq.c:30: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/seq.c:68:9: warning: unused variable 'iAux' [-Wunused-variable] int iAux; ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/symmatrix.c -o clustal/symmatrix.o In file included from clustal/symmatrix.c:30: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/tree.c -o clustal/tree.o In file included from clustal/tree.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/util.c -o clustal/util.o In file included from clustal/util.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal/weights.c -o clustal/weights.o In file included from clustal/weights.c:72: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/a2m.c -o squid/a2m.o In file included from squid/a2m.c:20: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/aligneval.c -o squid/aligneval.o In file included from squid/aligneval.c:59: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/alignio.c -o squid/alignio.o In file included from squid/alignio.c:21: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/clustal.c -o squid/clustal.o In file included from squid/clustal.c:24: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ squid/clustal.c:214:7: warning: unused variable 'cons' [-Wunused-variable] int cons; ^ squid/clustal.c:438:6: warning: unused variable 'cons' [-Wunused-variable] int cons; ^ 3 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/cluster.c -o squid/cluster.o In file included from squid/cluster.c:124: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/dayhoff.c -o squid/dayhoff.o In file included from squid/dayhoff.c:28: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/eps.c -o squid/eps.o In file included from squid/eps.c:23: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/file.c -o squid/file.o In file included from squid/file.c:28: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/getopt.c -o squid/getopt.o In file included from squid/getopt.c:17: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/gki.c -o squid/gki.o In file included from squid/gki.c:82: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/gsi.c -o squid/gsi.o In file included from squid/gsi.c:35: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/gsi64.c -o squid/gsi64.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/hsregex.c -o squid/hsregex.o In file included from squid/hsregex.c:33: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/iupac.c -o squid/iupac.o In file included from squid/iupac.c:17: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/msa.c -o squid/msa.o In file included from squid/msa.c:22: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/msf.c -o squid/msf.o In file included from squid/msf.c:25: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/phylip.c -o squid/phylip.o In file included from squid/phylip.c:23: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/revcomp.c -o squid/revcomp.o In file included from squid/revcomp.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/rk.c -o squid/rk.o In file included from squid/rk.c:26: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/selex.c -o squid/selex.o In file included from squid/selex.c:43: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/seqencode.c -o squid/seqencode.o In file included from squid/seqencode.c:18: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/shuffle.c -o squid/shuffle.o In file included from squid/shuffle.c:42: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/sqerror.c -o squid/sqerror.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/sqio.c -o squid/sqio.o In file included from squid/sqio.c:57: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/squidcore.c -o squid/squidcore.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/sre_ctype.c -o squid/sre_ctype.o In file included from squid/sre_ctype.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/sre_math.c -o squid/sre_math.o In file included from squid/sre_math.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/sre_random.c -o squid/sre_random.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/sre_string.c -o squid/sre_string.o In file included from squid/sre_string.c:23: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/ssi.c -o squid/ssi.o In file included from squid/ssi.c:16: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/stack.c -o squid/stack.o In file included from squid/stack.c:18: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/stockholm.c -o squid/stockholm.o In file included from squid/stockholm.c:31: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/stopwatch.c -o squid/stopwatch.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/translate.c -o squid/translate.o In file included from squid/translate.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/types.c -o squid/types.o In file included from squid/types.c:20: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/vectorops.c -o squid/vectorops.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c squid/weight.c -o squid/weight.o In file included from squid/weight.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c hhalign/hhalign.cpp -o hhalign/hhalign.o In file included from hhalign/hhalign.cpp:76: hhalign/hhhmm-C.h:344:60: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); break;} ^ hhalign/hhhmm-C.h:344:60: note: put the semicolon on a separate line to silence this warning hhalign/hhhmm-C.h:355:57: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); k--; break;} ^ hhalign/hhhmm-C.h:355:57: note: put the semicolon on a separate line to silence this warning In file included from hhalign/hhalign.cpp:77: hhalign/hhalignment-C.h:1908:43: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]<ANY) wi[k]=wg[k]; else wi[k]=0.0; ^ hhalign/hhalignment-C.h:2140:69: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0; ^ hhalign/hhalignment-C.h:2347:76: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ In file included from hhalign/hhalign.cpp:81: hhalign/hhhitlist-C.h:663:9: warning: address of array 'q.fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.') ~~^~~ ~~ hhalign/hhhitlist-C.h:840:9: warning: address of array 'q.fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.') ~~^~~ ~~ In file included from hhalign/hhalign.cpp:82: hhalign/hhfunc-C.h:74:9: warning: unused variable 'iT' [-Wunused-variable] int iT; /* transition state iterator */ ^ hhalign/hhfunc-C.h:80:11: warning: unused variable 'fGThgiew' [-Wunused-variable] float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */ ^ hhalign/hhfunc-C.h:85:11: warning: unused variable 'zf1SeqTrans' [-Wunused-variable] float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75}; ^ hhalign/hhfunc-C.h:86:11: warning: unused variable 'zf1SeqInit' [-Wunused-variable] float zf1SeqInit[] = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01}; ^ hhalign/hhfunc-C.h:87:11: warning: unused variable 'zf1SeqDel' [-Wunused-variable] float zf1SeqDel[] = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01}; ^ hhalign/hhfunc-C.h:88:11: warning: unused variable 'zf1SeqRevrt' [-Wunused-variable] float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01}; ^ hhalign/hhfunc-C.h:328:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable] const int NEFF_SCORE = 10; /* FIXME: Magic Number */ ^ hhalign/hhfunc-C.h:511:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable] const int NEFF_SCORE = 10; /* FIXME: Magic Number */ ^ 15 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c RClustalOmega.cpp -o RClustalOmega.o In file included from RClustalOmega.cpp:27: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c mymain.c -o mymain.o In file included from mymain.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC -Wall -g -O2 -c clustal-omega.c -o clustal-omega.o In file included from clustal-omega.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ <command line>:1:9: note: previous definition is here #define NDEBUG 1 ^ clustal-omega.c:134:58: warning: implicit conversion from 'double' to 'int' changes value from 0.01 to 0 [-Wliteral-conversion] static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^~~~ clustal-omega.c:134:18: warning: unused variable 'ITERATION_SCORE_IMPROVEMENT_THRESHOLD' [-Wunused-const-variable] static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01; ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o libClustalOmega.so exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation /Library/Developer/CommandLineTools/usr/bin/ranlib: file: libClustalOmega.a(gsi64.o) has no symbols ---------------------------------------- ------------- ClustalOmega ------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o msa.so R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: object file (./libgc.a(allchblk.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(alloc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(blacklst.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(checksums.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(dbg_mlc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(dyn_load.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(finalize.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(gc_dlopen.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(gcj_mlc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(headers.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(malloc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(mallocx.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(mark.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(mark_rts.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(misc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(new_hblk.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(obj_map.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(os_dep.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(pcr_interface.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(ptr_chck.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(real_malloc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(reclaim.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(specific.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(stubborn.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(typd_mlc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(backgraph.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(thread_local_alloc.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(pthread_start.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(pthread_support.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(pthread_stop_world.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(darwin_stop_world.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(atomic_ops.o)) was built for newer OSX version (10.14) than being linked (10.13) ld: warning: object file (./libgc.a(mach_dep.o)) was built for newer OSX version (10.14) than being linked (10.13) installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-msa/00new/msa/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (msa)
msa.Rcheck/msa-Ex.timings
name | user | system | elapsed | |
MsaMetaData-class | 0.768 | 0.061 | 0.834 | |
MsaMultipleAlignmentClasses | 0.376 | 0.032 | 0.409 | |
msa-package | 0.272 | 0.004 | 0.277 | |
msa | 0.730 | 0.024 | 0.756 | |
msaCheckNames | 0.066 | 0.003 | 0.068 | |
msaClustalOmega | 0.521 | 0.035 | 0.556 | |
msaClustalW | 0.512 | 0.005 | 0.518 | |
msaConsensusSequence-methods | 0.200 | 0.003 | 0.203 | |
msaConservationScore-methods | 1.614 | 0.062 | 1.686 | |
msaConvert | 0.257 | 0.046 | 0.304 | |
msaMuscle | 0.545 | 0.007 | 0.553 | |
msaPrettyPrint | 5.575 | 0.183 | 5.787 | |