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This page was generated on 2021-10-15 15:06:50 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the Rhdf5lib package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhdf5lib.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 1576/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rhdf5lib 1.14.2 (landing page) Mike Smith
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Rhdf5lib |
Version: 1.14.2 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhdf5lib |
StartedAt: 2021-10-14 08:17:59 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 08:22:17 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 258.5 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhdf5lib ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘Rhdf5lib’ ... ** using staged installation checking for gcc... clang -mmacosx-version-min=10.13 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 clang -mmacosx-version-min=10.13 accepts -g... yes checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes COMPILER = clang checking whether C++ compiler accepts -Wno-self-assign... yes checking whether C++ compiler accepts -Wno-bitwise-op-parentheses... yes checking whether C++ compiler accepts -Wno-cast-align -Wno-cast-qual... yes checking whether C++ compiler accepts -Wno-double-promotion... yes checking whether C++ compiler accepts -Wno-implicit-fallthrough... yes checking whether C++ compiler accepts -Wno-sometimes-uninitialized... yes checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory 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 zlib.h... yes checking curl/curl.h usability... yes checking curl/curl.h presence... yes checking for curl/curl.h... yes checking openssl/evp.h usability... no checking openssl/evp.h presence... no checking for openssl/evp.h... no checking openssl/hmac.h usability... no checking openssl/hmac.h presence... no checking for openssl/hmac.h... no checking openssl/sha.h usability... no checking openssl/sha.h presence... no checking for openssl/sha.h... no S3_VFD=--enable-ros3-vfd=no untarring hdf5small_cxx_hl_1.10.7.tar.gz ... building the szip library... checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... bin/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 build system type... x86_64-apple-darwin18.7.0 checking host system type... x86_64-apple-darwin18.7.0 checking for config x86_64-apple-darwin18.7.0... no checking for config x86_64-apple-darwin18.7.0... no checking for config apple-darwin18.7.0... no checking for config apple-darwin18.7.0... no checking for config x86_64-darwin18.7.0... no checking for config x86_64-darwin18.7.0... no checking for config x86_64-apple... no checking for config darwin18.7.0... no checking for config darwin18.7.0... no checking for config apple... no checking for config x86_64... no checking for gcc... clang -mmacosx-version-min=10.13 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 clang -mmacosx-version-min=10.13 accepts -g... yes checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed checking whether clang -mmacosx-version-min=10.13 understands -c and -o together... rm: conftest.dSYM: is a directory yes checking for style of include used by make... GNU checking dependency style of clang -mmacosx-version-min=10.13... gcc3 checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E checking whether make sets $(MAKE)... (cached) yes 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 clang -mmacosx-version-min=10.13... /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... rm: conftest.dSYM: is a directory 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 archiver @FILE support... rm: conftest.dSYM: is a directory no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 object... rm: conftest.dSYM: is a directory ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 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 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 clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes checking if clang -mmacosx-version-min=10.13 static flag -static works... no checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes checking whether the clang -mmacosx-version-min=10.13 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 for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for build mode... production checking for math library support... no checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for error_at_line... no checking for working memcmp... yes checking for vprintf... yes checking for _doprnt... no checking for memset... yes checking if encoding enabled... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/SZconfig.h config.status: executing depfiles commands config.status: executing libtool commands Making all in src make all-am /bin/sh ../libtool --tag=CC --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I/usr/local/include -Wall -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c libtool: compile: clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I/usr/local/include -Wall -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c -fno-common -DPIC -o rice.o mv -f .deps/rice.Tpo .deps/rice.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I/usr/local/include -Wall -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c libtool: compile: clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I/usr/local/include -Wall -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c -fno-common -DPIC -o sz_api.o mv -f .deps/sz_api.Tpo .deps/sz_api.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I/usr/local/include -Wall -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c libtool: compile: clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I/usr/local/include -Wall -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c -fno-common -DPIC -o encoding.o mv -f .deps/encoding.Tpo .deps/encoding.Plo /bin/sh ../libtool --tag=CC --mode=link clang -mmacosx-version-min=10.13 -Wall -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC -version-info 2:0:0 -o libsz.la -rpath /Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo -lm libtool: link: ar cru .libs/libsz.a rice.o sz_api.o encoding.o libtool: link: ranlib .libs/libsz.a libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" ) make[1]: Nothing to be done for `all-am'. Making install in src ../bin/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libsz.la '/Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib' libtool: install: /usr/bin/install -c .libs/libsz.lai /Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la libtool: install: /usr/bin/install -c .libs/libsz.a /Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a libtool: install: chmod 644 /Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a libtool: install: ranlib /Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a ../bin/install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include' /usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. building the hdf5 library... checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... bin/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 make supports nested variables... (cached) yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-apple-darwin18.7.0 checking host system type... x86_64-apple-darwin18.7.0 checking shell variables initial values... done checking if basename works... yes checking if xargs works... yes checking for cached host... none checking for config x86_64-apple-darwin18.7.0... no checking for config x86_64-apple-darwin18.7.0... no checking for config apple-darwin18.7.0... no checking for config apple-darwin18.7.0... no checking for config x86_64-darwin18.7.0... no checking for config x86_64-darwin18.7.0... no checking for config x86_64-apple... no checking for config darwin18.7.0... no checking for config darwin18.7.0... no checking for config apple... found compiler 'clang -mmacosx-version-min=10.13' is Apple LLVM-10.0.1 No match to get cc_version_info for clang -mmacosx-version-min=10.13 compiler 'gfortran' is GNU gfortran-8.2.0 checking for config ./config/site-specific/host-machv2.bioconductor.org... no checking for config ./config/site-specific/host-bioconductor.org... no checking for config ./config/site-specific/host-org... no checking for clang sanitizer checks... none checking build mode... production checking for gcc... clang -mmacosx-version-min=10.13 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 clang -mmacosx-version-min=10.13 accepts -g... yes checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed checking whether clang -mmacosx-version-min=10.13 understands -c and -o together... rm: conftest.dSYM: is a directory yes checking for style of include used by make... 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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 archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 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 for dlfcn.h... yes checking for objdir... .libs checking if clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes checking if clang -mmacosx-version-min=10.13 static flag -static works... no checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes checking whether the clang -mmacosx-version-min=10.13 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 for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++14 -E checking for ld used by clang++ -mmacosx-version-min=10.13 -std=gnu++14... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for clang++ -mmacosx-version-min=10.13 -std=gnu++14 option to produce PIC... -fno-common -DPIC checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 PIC flag -fno-common -DPIC works... yes checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 static flag -static works... no checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... yes checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... 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int16_t... 2 checking size of uint16_t... 2 checking size of int_least16_t... 2 checking size of uint_least16_t... 2 checking size of int_fast16_t... 2 checking size of uint_fast16_t... 2 checking size of int32_t... 4 checking size of uint32_t... 4 checking size of int_least32_t... 4 checking size of uint_least32_t... 4 checking size of int_fast32_t... 4 checking size of uint_fast32_t... 4 checking size of int64_t... 8 checking size of uint64_t... 8 checking size of int_least64_t... 8 checking size of uint_least64_t... 8 checking size of int_fast64_t... 8 checking size of uint_fast64_t... 8 checking size of size_t... 8 checking size of ssize_t... 8 checking size of ptrdiff_t... 8 checking size of off_t... 8 checking size of bool... 1 checking size of time_t... 8 checking if dev_t is scalar... yes checking for dmalloc library... suppressed checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for compress2 in -lz... yes checking for compress2... yes checking for SZ_BufftoBuffCompress in -lsz... yes checking szlib.h usability... yes checking szlib.h presence... yes checking for szlib.h... yes checking for szlib encoder... yes checking for thread safe support... no checking whether CLOCK_MONOTONIC is declared... yes checking for tm_gmtoff in struct tm... yes checking for global timezone variable... yes checking for st_blocks in struct stat... no checking for _getvideoconfig... no checking for gettextinfo... no checking for GetConsoleScreenBufferInfo... no checking for getpwuid... yes checking for _scrsize... no checking for ioctl... yes checking for struct videoconfig... no checking for struct text_info... no checking for TIOCGWINSZ... yes checking for TIOCGETD... yes checking for library containing clock_gettime... none required checking for alarm... yes checking for clock_gettime... yes checking for difftime... yes checking for fcntl... yes checking for flock... yes checking for fork... yes checking for frexpf... yes checking for frexpl... yes checking for gethostname... yes checking for getrusage... yes checking for gettimeofday... yes checking for lstat... yes checking for rand_r... yes checking for random... yes checking for setsysinfo... no checking for signal... yes checking for longjmp... yes checking for setjmp... yes checking for siglongjmp... yes checking for sigsetjmp... yes checking for sigprocmask... yes checking for snprintf... yes checking for srandom... yes checking for strdup... yes checking for symlink... yes checking for system... yes checking for strtoll... yes checking for strtoull... yes checking for tmpfile... yes checking for asprintf... yes checking for vasprintf... yes checking for vsnprintf... yes checking for waitpid... yes checking for roundf... yes checking for lroundf... yes checking for llroundf... yes checking for round... yes checking for lround... yes checking for llround... yes checking for an ANSI C-conforming const... yes checking if the compiler understands __inline__... yes checking if the compiler understands __inline... yes checking if the compiler understands inline... yes checking for __attribute__ extension... yes checking for __func__ extension... yes checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %ld and %lu checking enable debugging symbols... no checking enable asserts... no checking enable developer warnings... no checking profiling... no checking optimization level... high checking enable file locking... best-effort checking for internal debug output... none checking whether function stack tracking is enabled... no checking for API tracing... no checking whether a memory checking tool will be used... no checking whether internal memory allocation sanity checking is used... no checking for parallel support files... skipped checking whether O_DIRECT is declared... no checking for posix_memalign... yes checking if the direct I/O virtual file driver (VFD) is enabled... no checking if the Mirror virtual file driver (VFD) is enabled... no checking if the Read-Only S3 virtual file driver (VFD) is enabled... no checking for libhdfs... suppressed checking for custom examples path definition... ${prefix}/share/hdf5_examples checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin checking whether exception handling functions is checked during data conversions... yes checking whether data accuracy is guaranteed during data conversions... yes checking if the machine has window style path name... no checking if using special algorithm to convert long double to (unsigned) long values... no checking if using special algorithm to convert (unsigned) long to long double values... no checking if correctly converting long double to (unsigned) long long values... yes checking if correctly converting (unsigned) long long to long double values... yes checking if the system is IBM ppc64le and cannot correctly convert some long double values... no checking additional programs should be built... no checking if deprecated public symbols are available... yes checking which version of public symbols to use by default... v110 checking whether to perform strict file format checks... no checking for pread... yes checking for pwrite... yes checking whether to use pread/pwrite instead of read/write in certain VFDs... yes checking whether to have library information embedded in the executables... yes checking if alignment restrictions are strictly enforced... no configure: creating ./config.lt config.lt: creating libtool checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating src/libhdf5.settings config.status: creating Makefile config.status: creating src/Makefile config.status: creating utils/Makefile config.status: creating utils/mirror_vfd/Makefile config.status: creating bin/h5cc config.status: creating bin/Makefile config.status: creating c++/Makefile config.status: creating c++/src/Makefile config.status: creating c++/src/h5c++ config.status: creating hl/Makefile config.status: creating hl/src/Makefile config.status: creating hl/c++/Makefile config.status: creating hl/c++/src/Makefile config.status: creating src/H5config.h config.status: executing pubconf commands creating src/H5pubconf.h Post process src/libhdf5.settings config.status: executing depfiles commands config.status: executing libtool commands config.status: executing .classes commands sed: -i may not be used with stdin SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.10.7 Configured on: Thu Oct 14 08:18:41 EDT 2021 Configured by: biocbuild@machv2.bioconductor.org Host system: x86_64-apple-darwin18.7.0 Uname information: Darwin machv2.bioconductor.org 18.7.0 Darwin Kernel Version 18.7.0: Mon Aug 31 20:53:32 PDT 2020; root:xnu-4903.278.44~1/RELEASE_X86_64 x86_64 Byte sex: little-endian Installation point: /Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/hdf5 Compiling Options: ------------------ Build Mode: production Debugging Symbols: no Asserts: no Profiling: no Optimization Level: high Linking Options: ---------------- Libraries: static Statically Linked Executables: LDFLAGS: -L/usr/local/lib H5_LDFLAGS: AM_LDFLAGS: -L/Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib Extra libraries: -lsz -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: ranlib Languages: ---------- C: yes C Compiler: /usr/bin/clang -mmacosx-version-min=10.13 CPPFLAGS: -I/usr/local/include H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/Users/biocbuild/bbs-3.13-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include C Flags: -Wall -g -O2 -Wno-self-assign -Wno-bitwise-op-parentheses -Wno-cast-align -Wno-cast-qual -Wno-double-promotion -Wno-implicit-fallthrough -Wno-sometimes-uninitialized -fPIC H5 C Flags: -std=c99 -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wno-c++-compat -Wno-format-nonliteral -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wvolatile-register-var -Wno-self-assign-overloaded -Wno-unknown-warning-option -Wno-missing-noreturn -O3 -Werror=bad-function-cast -Werror=implicit-function-declaration -Werror=incompatible-pointer-types -Werror=missing-declarations -Werror=packed -Werror=shadow -Werror=switch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat AM C Flags: Shared C Library: no Static C Library: yes Fortran: no C++: yes C++ Compiler: /usr/bin/clang++ -mmacosx-version-min=10.13 -std=gnu++14 C++ Flags: -Wall -g -O2 -fPIC H5 C++ Flags: AM C++ Flags: Shared C++ Library: no Static C++ Library: yes Java: no Features: --------- Parallel HDF5: no Parallel Filtered Dataset Writes: no Large Parallel I/O: no High-level library: yes Build HDF5 Tests: yes Build HDF5 Tools: yes Threadsafety: no Default API mapping: v110 With deprecated public symbols: yes I/O filters (external): deflate(zlib),szip(encoder) MPE: no Direct VFD: no Mirror VFD: no (Read-Only) S3 VFD: no (Read-Only) HDFS VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no for d in src . c++ hl; do \ if test $d != .; then \ (cd $d && make lib) || exit 1; \ fi; \ done CC H5.lo CC H5checksum.lo CC H5dbg.lo CC H5system.lo CC H5timer.lo CC H5trace.lo CC H5A.lo CC H5Abtree2.lo CC H5Adense.lo H5Adense.c:314:16: warning: initializing 'H5A_t *' (aka 'struct H5A_t *') with an expression of type 'const H5A_t *' (aka 'const struct H5A_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] H5A_t *old_attr = *user_attr; ^ ~~~~~~~~~~ 1 warning generated. CC H5Adeprec.lo CC H5Aint.lo CC H5Atest.lo CC H5AC.lo CC H5ACdbg.lo CC H5ACproxy_entry.lo CC H5B.lo CC H5Bcache.lo CC H5Bdbg.lo CC H5B2.lo CC H5B2cache.lo CC H5B2dbg.lo CC H5B2hdr.lo CC H5B2int.lo CC H5B2internal.lo CC H5B2leaf.lo CC H5B2stat.lo CC H5B2test.lo CC H5C.lo H5C.c:4359:5: warning: unused variable 'err_occurred' [-Wunused-variable] FUNC_ENTER_STATIC ^ ./H5private.h:2350:5: note: expanded from macro 'FUNC_ENTER_STATIC' FUNC_ENTER_COMMON(H5_IS_PKG(FUNC)); \ ^ ./H5private.h:2130:13: note: expanded from macro 'FUNC_ENTER_COMMON' hbool_t err_occurred = FALSE; \ ^ H5C.c:4376:1: warning: unused label 'done' [-Wunused-label] done: ^~~~~ 2 warnings generated. CC H5Cdbg.lo CC H5Cepoch.lo CC H5Cimage.lo CC H5Clog.lo CC H5Clog_json.lo CC H5Clog_trace.lo CC H5Cprefetched.lo CC H5Cquery.lo CC H5Ctag.lo CC H5Ctest.lo CC H5CS.lo CC H5CX.lo CC H5D.lo CC H5Dbtree.lo CC H5Dbtree2.lo CC H5Dchunk.lo H5Dchunk.c:1873:38: warning: passing 'const H5S_t *' (aka 'const struct H5S_t *') to parameter of type 'H5S_t *' (aka 'struct H5S_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] if(H5S_combine_hyperslab(fm->file_space, H5S_SELECT_AND, coords, NULL, fm->chunk_dim, NULL, &tmp_fchunk) < 0) ^~~~~~~~~~~~~~ ./H5Sprivate.h:313:44: note: passing argument to parameter 'old_space' here H5_DLL herr_t H5S_combine_hyperslab(H5S_t *old_space, H5S_seloper_t op, ^ H5Dchunk.c:4482:22: warning: assigning to 'H5O_storage_chunk_t *' (aka 'struct H5O_storage_chunk_t *') from 'const H5O_storage_chunk_t *' (aka 'const struct H5O_storage_chunk_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] idx_info.storage = sc; ^ ~~ H5Dchunk.c:6159:95: warning: passing 'const hsize_t *' (aka 'const unsigned long long *') to parameter of type 'hsize_t *' (aka 'unsigned long long *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] if(H5D__chunk_file_alloc(udata->idx_info_dst, NULL, &udata_dst.chunk_block, &need_insert, udata_dst.common.scaled) < 0) ^~~~~~~~~~~~~~~~~~~~~~~ ./H5Dpkg.h:653:59: note: passing argument to parameter 'scaled' here H5F_block_t *new_chunk, hbool_t *need_insert, hsize_t scaled[]); ^ 3 warnings generated. CC H5Dcompact.lo CC H5Dcontig.lo CC H5Ddbg.lo CC H5Ddeprec.lo CC H5Dearray.lo CC H5Defl.lo CC H5Dfarray.lo CC H5Dfill.lo CC H5Dint.lo H5Dint.c:2230:5: warning: returning 'const H5G_name_t *' from a function with result type 'H5G_name_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : NULL) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./H5private.h:2437:11: note: expanded from macro 'FUNC_LEAVE_NOAPI' return(ret_value); \ ^~~~~~~~~~~ H5Dint.c:3327:52: warning: passing 'const H5F_t *' (aka 'const struct H5F_t *') to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] if(H5I_iterate(H5I_DATASET, H5D__flush_all_cb, f, FALSE) < 0) /* Casting away const OK -QAK */ ^ ./H5Iprivate.h:70:74: note: passing argument to parameter 'udata' here H5_DLL herr_t H5I_iterate(H5I_type_t type, H5I_search_func_t func, void *udata, hbool_t app_ref); ^ 2 warnings generated. CC H5Dio.lo CC H5Dlayout.lo CC H5Dnone.lo CC H5Doh.lo CC H5Dscatgath.lo CC H5Dselect.lo CC H5Dsingle.lo CC H5Dtest.lo CC H5Dvirtual.lo CC H5E.lo CC H5Edeprec.lo CC H5Eint.lo CC H5EA.lo CC H5EAcache.lo CC H5EAdbg.lo CC H5EAdblkpage.lo CC H5EAdblock.lo CC H5EAhdr.lo CC H5EAiblock.lo CC H5EAint.lo CC H5EAsblock.lo CC H5EAstat.lo CC H5EAtest.lo CC H5F.lo CC H5Faccum.lo CC H5Fcwfs.lo CC H5Fdbg.lo CC H5Fdeprec.lo CC H5Fefc.lo CC H5Ffake.lo CC H5Fint.lo CC H5Fio.lo CC H5Fmount.lo CC H5Fquery.lo CC H5Fsfile.lo CC H5Fspace.lo CC H5Fsuper.lo CC H5Fsuper_cache.lo CC H5Ftest.lo CC H5FA.lo CC H5FAcache.lo CC H5FAdbg.lo CC H5FAdblock.lo CC H5FAdblkpage.lo CC H5FAhdr.lo CC H5FAint.lo CC H5FAstat.lo CC H5FAtest.lo CC H5FD.lo CC H5FDcore.lo CC H5FDfamily.lo CC H5FDhdfs.lo H5FDhdfs.c:1761:24: warning: unused parameter 'fapl_id' [-Wunused-parameter] H5Pget_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa_out) ^ H5FDhdfs.c:1761:51: warning: unused parameter 'fa_out' [-Wunused-parameter] H5Pget_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa_out) ^ H5FDhdfs.c:1775:24: warning: unused parameter 'fapl_id' [-Wunused-parameter] H5Pset_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa) ^ H5FDhdfs.c:1775:51: warning: unused parameter 'fa' [-Wunused-parameter] H5Pset_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa) ^ 4 warnings generated. CC H5FDint.lo CC H5FDlog.lo CC H5FDmulti.lo CC H5FDsec2.lo CC H5FDspace.lo CC H5FDsplitter.lo CC H5FDstdio.lo CC H5FDtest.lo CC H5FL.lo CC H5FO.lo CC H5FS.lo CC H5FScache.lo H5FScache.c:1235:66: warning: unused parameter 'len' [-Wunused-parameter] H5FS__cache_sinfo_serialize(const H5F_t *f, void *_image, size_t len, ^ 1 warning generated. CC H5FSdbg.lo CC H5FSint.lo CC H5FSsection.lo CC H5FSstat.lo CC H5FStest.lo CC H5G.lo CC H5Gbtree2.lo CC H5Gcache.lo CC H5Gcompact.lo CC H5Gdense.lo CC H5Gdeprec.lo CC H5Gent.lo CC H5Gint.lo CC H5Glink.lo CC H5Gloc.lo CC H5Gname.lo CC H5Gnode.lo H5Gnode.c:756:22: warning: unused variable 'lt_key' [-Wunused-variable] H5G_node_key_t *lt_key = (H5G_node_key_t *)_lt_key; ^ 1 warning generated. CC H5Gobj.lo CC H5Goh.lo CC H5Groot.lo CC H5Gstab.lo CC H5Gtest.lo CC H5Gtraverse.lo CC H5HF.lo CC H5HFbtree2.lo CC H5HFcache.lo H5HFcache.c:770:12: warning: assigning to 'H5F_t *' (aka 'struct H5F_t *') from 'const H5F_t *' (aka 'const struct H5F_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] hdr->f = f; ^ ~ H5HFcache.c:1360:12: warning: assigning to 'H5F_t *' (aka 'struct H5F_t *') from 'const H5F_t *' (aka 'const struct H5F_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] hdr->f = f; ^ ~ 2 warnings generated. CC H5HFdbg.lo CC H5HFdblock.lo CC H5HFdtable.lo CC H5HFhdr.lo CC H5HFhuge.lo H5HFhuge.c:124:36: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32] bt2_cparam.rrec_size = (size_t)((unsigned)hdr->sizeof_addr /* Address of object */ ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5HFhuge.c:131:36: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32] bt2_cparam.rrec_size = (size_t)((unsigned)hdr->sizeof_addr /* Address of object */ ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5HFhuge.c:138:36: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32] bt2_cparam.rrec_size = (size_t)((unsigned)hdr->sizeof_addr /* Address of filtered object */ ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5HFhuge.c:146:36: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'uint32_t' (aka 'unsigned int') [-Wshorten-64-to-32] bt2_cparam.rrec_size = (size_t)((unsigned)hdr->sizeof_addr /* Address of object */ ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 warnings generated. CC H5HFiblock.lo CC H5HFiter.lo CC H5HFman.lo CC H5HFsection.lo CC H5HFspace.lo CC H5HFstat.lo CC H5HFtest.lo CC H5HFtiny.lo CC H5HG.lo CC H5HGcache.lo CC H5HGdbg.lo CC H5HGquery.lo CC H5HL.lo CC H5HLcache.lo CC H5HLdbg.lo CC H5HLint.lo CC H5HLprfx.lo CC H5HLdblk.lo CC H5HP.lo CC H5I.lo H5I.c:2135:31: warning: passing 'const H5G_t *' (aka 'const struct H5G_t *') to parameter of type 'H5G_t *' (aka 'struct H5G_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] path = H5G_nameof((const H5G_t *)item->obj_ptr); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./H5Gprivate.h:190:39: note: passing argument to parameter 'grp' here H5_DLL H5G_name_t * H5G_nameof(H5G_t *grp); ^ H5I.c:125:12: warning: unused function 'H5I__debug_cb' [-Wunused-function] static int H5I__debug_cb(void *_item, void *_key, void *_udata); ^ 2 warnings generated. CC H5Itest.lo CC H5L.lo CC H5Lexternal.lo CC H5make_libsettings.o CCLD H5make_libsettings LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/lib | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5make_libsettings > H5lib_settings.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5lib_settings.c ; exit 1) CC H5lib_settings.lo CC H5MF.lo CC H5MFaggr.lo CC H5MFdbg.lo CC H5MFsection.lo CC H5MM.lo CC H5MP.lo CC H5MPtest.lo CC H5O.lo H5O.c:1169:17: warning: unused variable 'obj_oloc' [-Wunused-variable] H5O_loc_t obj_oloc; /* Opened object object location */ ^ H5O.c:1168:17: warning: unused variable 'obj_path' [-Wunused-variable] H5G_name_t obj_path; /* Opened object group hier. path */ ^ 2 warnings generated. CC H5Odeprec.lo H5Odeprec.c:174:17: warning: unused variable 'obj_path' [-Wunused-variable] H5G_name_t obj_path; /* Opened object group hier. path */ ^ H5Odeprec.c:175:17: warning: unused variable 'obj_oloc' [-Wunused-variable] H5O_loc_t obj_oloc; /* Opened object object location */ ^ 2 warnings generated. CC H5Oainfo.lo H5Oainfo.c:333:36: warning: unused parameter 'open_oh' [-Wunused-parameter] H5O__ainfo_delete(H5F_t *f, H5O_t *open_oh, void *_mesg) ^ H5Oainfo.c:404:29: warning: unused parameter 'file_src' [-Wunused-parameter] H5O__ainfo_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst, ^ H5Oainfo.c:406:17: warning: unused parameter 'cpy_info' [-Wunused-parameter] H5O_copy_t *cpy_info, void H5_ATTR_UNUSED *udata) ^ 3 warnings generated. CC H5Oalloc.lo H5Oalloc.c:113:20: warning: unused parameter 'f' [-Wunused-parameter] H5O_add_gap(H5F_t *f, H5O_t *oh, unsigned chunkno, hbool_t *chk_dirtied, ^ 1 warning generated. CC H5Oattr.lo CC H5Oattribute.lo CC H5Obogus.lo CC H5Obtreek.lo CC H5Ocache.lo CC H5Ocache_image.lo H5Ocache_image.c:278:35: warning: unused parameter 'open_oh' [-Wunused-parameter] H5O__mdci_delete(H5F_t *f, H5O_t *open_oh, void *_mesg) ^ 1 warning generated. CC H5Ochunk.lo CC H5Ocont.lo CC H5Ocopy.lo CC H5Odbg.lo CC H5Odrvinfo.lo CC H5Odtype.lo CC H5Oefl.lo CC H5Ofill.lo CC H5Oflush.lo CC H5Ofsinfo.lo CC H5Oginfo.lo CC H5Oint.lo H5Oint.c:278:22: warning: unused variable 'oc_plist' [-Wunused-variable] H5P_genplist_t *oc_plist; /* Object creation property list */ ^ H5Oint.c:284:17: warning: unused variable 'insert_flags' [-Wunused-variable] unsigned insert_flags = H5AC__NO_FLAGS_SET; /* Flags for inserting objec t header into cache */ ^ H5Oint.c:281:17: warning: unused variable 'oh_addr' [-Wunused-variable] haddr_t oh_addr; /* Address of initial object header */ ^ H5Oint.c:283:16: warning: unused variable 'oh_flags' [-Wunused-variable] uint8_t oh_flags; /* Object header's initial status flags */ ^ H5Oint.c:282:17: warning: unused variable 'oh_size' [-Wunused-variable] size_t oh_size; /* Size of initial object header */ ^ H5Oint.c:285:17: warning: unused variable 'store_msg_crt_idx' [-Wunused-variable] hbool_t store_msg_crt_idx; /* Whether to always store message crea tion indices for this file */ ^ 6 warnings generated. CC H5Olayout.lo CC H5Olinfo.lo CC H5Olink.lo CC H5Omessage.lo CC H5Omtime.lo CC H5Oname.lo CC H5Onull.lo CC H5Opline.lo CC H5Orefcount.lo CC H5Osdspace.lo CC H5Oshared.lo H5Oshared.c:585:30: warning: unused parameter 'file_src' [-Wunused-parameter] H5O__shared_copy_file(H5F_t *file_src, H5F_t *file_dst, ^ H5Oshared.c:587:79: warning: unused parameter 'cpy_info' [-Wunused-parameter] hbool_t H5_ATTR_UNUSED *recompute_size, unsigned *mesg_flags, H5O_copy_t *cpy_info, ^ 2 warnings generated. CC H5Oshmesg.lo CC H5Ostab.lo CC H5Otest.lo CC H5Ounknown.lo CC H5P.lo CC H5Pacpl.lo CC H5Pdapl.lo CC H5Pdcpl.lo CC H5Pdeprec.lo CC H5Pdxpl.lo CC H5Pencdec.lo CC H5Pfapl.lo CC H5Pfcpl.lo CC H5Pfmpl.lo CC H5Pgcpl.lo CC H5Pint.lo CC H5Plapl.lo CC H5Plcpl.lo CC H5Pocpl.lo CC H5Pocpypl.lo CC H5Pstrcpl.lo CC H5Ptest.lo CC H5PB.lo CC H5PL.lo CC H5PLint.lo CC H5PLpath.lo CC H5PLplugin_cache.lo CC H5R.lo CC H5Rint.lo H5Rint.c:709:31: warning: unused parameter 'id' [-Wunused-parameter] H5R__get_name(H5F_t *f, hid_t id, H5R_type_t ref_type, const void *_ref, ^ 1 warning generated. CC H5Rdeprec.lo CC H5UC.lo CC H5RS.lo CC H5S.lo CC H5Sall.lo CC H5Sdbg.lo CC H5Shyper.lo H5Shyper.c:3531:1: warning: unused function 'H5S__hyper_get_enc_size_real' [-Wunused-function] H5S__hyper_get_enc_size_real(hsize_t max_size) ^ 1 warning generated. CC H5Snone.lo CC H5Spoint.lo CC H5Sselect.lo CC H5Stest.lo CC H5SL.lo CC H5SM.lo CC H5SMbtree2.lo CC H5SMcache.lo CC H5SMmessage.lo CC H5SMtest.lo CC H5ST.lo CC H5T.lo H5T.c:5246:23: warning: assigning to 'H5G_name_t *' from 'const H5G_name_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] ret_value = &(dt->path); ^ ~~~~~~~~~~~ 1 warning generated. CC H5Tarray.lo CC H5Tbit.lo CC H5Tcommit.lo CC H5Tcompound.lo CC H5Tconv.lo CC H5Tcset.lo CC H5Tdbg.lo CC H5Tdeprec.lo CC H5Tenum.lo CC H5Tfields.lo CC H5Tfixed.lo CC H5Tfloat.lo CC H5detect.o CCLD H5detect LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/lib | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5detect > H5Tinit.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5Tinit.c ; exit 1) CC H5Tinit.lo CC H5Tnative.lo CC H5Toffset.lo CC H5Toh.lo CC H5Topaque.lo CC H5Torder.lo CC H5Tpad.lo CC H5Tprecis.lo CC H5Tstrpad.lo CC H5Tvisit.lo CC H5Tvlen.lo CC H5TS.lo CC H5VM.lo CC H5WB.lo CC H5Z.lo H5Z.c:108:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion] H5Z_SZIP->encoder_present = SZ_encoder_enabled(); ~ ^~~~~~~~~~~~~~~~~~~~ 1 warning generated. CC H5Zdeflate.lo CC H5Zfletcher32.lo CC H5Znbit.lo CC H5Zshuffle.lo CC H5Zscaleoffset.lo H5Zscaleoffset.c:1125:19: warning: implicit conversion changes signedness: 'H5T_order_t' (aka 'enum H5T_order_t') to 'unsigned int' [-Wsign-conversion] p.mem_order = H5T_native_order_g; ~ ^~~~~~~~~~~~~~~~~~ 1 warning generated. CC H5Zszip.lo H5Zszip.c:90:25: warning: implicit conversion loses integer precision: 'unsigned long' to 'unsigned int' [-Wshorten-64-to-32] if((dtype_size = (8 * H5T_get_size(type))) == 0) ~ ~~^~~~~~~~~~~~~~~~~~~~ H5Zszip.c:165:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] dtype_offset = H5T_get_offset(type); ~ ^~~~~~~~~~~~~~~~~~~~ H5Zszip.c:206:85: warning: operand of ? changes signedness: 'hssize_t' (aka 'long long') to 'hsize_t' (aka 'unsigned long long') [-Wsign-conversion] scanline = MIN((cd_values[H5Z_SZIP_PARM_PPB] * SZ_MAX_BLOCKS_PER_SCANLINE), npoints); ~ ^~~~~~~ ./H5private.h:408:41: note: expanded from macro 'MIN' #define MIN(a,b) (((a)<(b)) ? (a) : (b)) ^ H5Zszip.c:224:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion] cd_values[H5Z_SZIP_PARM_MASK] &= ~(SZ_LSB_OPTION_MASK|SZ_MSB_OPTION_MASK); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5Zszip.c:177:36: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32] cd_values[H5Z_SZIP_PARM_BPP] = dtype_precision; ~ ^~~~~~~~~~~~~~~ 5 warnings generated. CC H5Ztrans.lo CCLD libhdf5.la /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols make[2]: Nothing to be done for `build-lib'. + cd src + make lib CXX H5Exception.lo CXX H5IdComponent.lo CXX H5DataSpace.lo CXX H5PropList.lo CXX H5Library.lo CXX H5FaccProp.lo CXX H5FcreatProp.lo CXX H5LcreatProp.lo CXX H5LaccProp.lo CXX H5DaccProp.lo CXX H5DxferProp.lo CXX H5DcreatProp.lo CXX H5Location.lo CXX H5AbstractDs.lo CXX H5Attribute.lo CXX H5Object.lo CXX H5OcreatProp.lo CXX H5DataType.lo CXX H5AtomType.lo CXX H5PredType.lo CXX H5EnumType.lo CXX H5IntType.lo CXX H5FloatType.lo CXX H5StrType.lo CXX H5ArrayType.lo CXX H5VarLenType.lo CXX H5CompType.lo CXX H5DataSet.lo CXX H5CommonFG.lo CXX H5Group.lo CXX H5File.lo CXXLD libhdf5_cpp.la make[2]: Nothing to be done for `build-lib'. + cd src + make lib CC H5DO.lo CC H5DS.lo CC H5IM.lo CC H5LT.lo CC H5LTanalyze.lo CC H5LTparse.lo CC H5PT.lo CC H5TB.lo CC H5LD.lo CCLD libhdf5_hl.la + cd c++ + make lib make[3]: Nothing to be done for `build-lib'. + cd src + make lib CXX H5PacketTable.lo CXXLD libhdf5_hl_cpp.la test passed configure: HDF5_INCLUDE=hdf5/src configure: HDF5_CXX_INCLUDE=hdf5/c++/src configure: HDF5_HL_INCLUDE=hdf5/hl/src configure: HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src configure: HDF5_LIB=hdf5/src/.libs/libhdf5.a configure: HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a configure: HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a configure: HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a configure: SZIP_LIB=hdf5/szip/src/.libs/libsz.a configure: creating ./config.status config.status: creating src/Makevars ** libs mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src/"*.h "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/c++/src/"*.h "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/src/"*.h "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/c++/src/"*.h "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src/"libhdf5.settings "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/src/.libs/libhdf5.a" "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/szip/src/.libs/libsz.a" "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Ihdf5/src -I/usr/local/include -fPIC -Wall -g -O2 -c Rhdf5lib.c -o Rhdf5lib.o clang -mmacosx-version-min=10.13 -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 Rhdf5lib.so Rhdf5lib.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/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 (Rhdf5lib)