Rdisop 1.8.0
Steffen Neumann
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/Rdisop | | Last Changed Rev: 46401 / Revision: 49923 | | Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | N O T S U P P O R T E D |
| pelham | Mac OS X Leopard (10.5.8) / i386 | N O T S U P P O R T E D |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/Rdisop.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rdisop/DESCRIPTION' ... OK
* this is package 'Rdisop' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rdisop' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package 'Rdisop' ...
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for IMS... checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 ANSI C... none needed
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /usr/x86_64-suse-linux/bin/ld
checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
checking for /usr/x86_64-suse-linux/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
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checking dlfcn.h usability... yes
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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 how to run the C++ preprocessor... g++ -E
checking for g77... no
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checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
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checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/x86_64-suse-linux/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
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
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/x86_64-suse-linux/bin/ld
checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking whether the gfortran linker (/usr/x86_64-suse-linux/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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 for cppunit-config... no
checking for Cppunit - version >= 1.8.0... configure: WARNING: Cppunit not found, make check will not work
checking for round in -lm... yes
checking for floor in -lm... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating libims.pc
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing headercreation commands
config.status: creating src/ims/utils/math.h
imslib configuration:
Compiler: g++
Linker: /usr/x86_64-suse-linux/bin/ld
Compiler flags: -Wall -W -Wwrite-strings -Wundef -g -O2
Preprocessor flags:
Linker flags:
CppUnit available: no
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -fpic -g -O2 -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fpic -g -O2 -c disop.cpp -o disop.o
disop.cpp: In function 'void initializeAlphabet(SEXPREC*, alphabet_t&, int)':
disop.cpp:797: warning: deprecated conversion from string constant to 'char*'
disop.cpp:799: warning: deprecated conversion from string constant to 'char*'
disop.cpp:801: warning: deprecated conversion from string constant to 'char*'
disop.cpp:803: warning: deprecated conversion from string constant to 'char*'
disop.cpp:804: warning: deprecated conversion from string constant to 'char*'
disop.cpp:805: warning: deprecated conversion from string constant to 'char*'
make -C imslib src/libims.la
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.6-bioc/meat/Rdisop.Rcheck/00_pkg_src/Rdisop/src/imslib'
depbase=`echo src/ims/element.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/element.lo src/ims/element.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF src/ims/.deps/element.Tpo -c src/ims/element.cpp -fPIC -DPIC -o src/ims/.libs/element.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF src/ims/.deps/element.Tpo -c src/ims/element.cpp -o src/ims/element.o >/dev/null 2>&1
depbase=`echo src/ims/composedelement.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/composedelement.lo src/ims/composedelement.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF src/ims/.deps/composedelement.Tpo -c src/ims/composedelement.cpp -fPIC -DPIC -o src/ims/.libs/composedelement.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF src/ims/.deps/composedelement.Tpo -c src/ims/composedelement.cpp -o src/ims/composedelement.o >/dev/null 2>&1
depbase=`echo src/ims/isotopedistribution.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/isotopedistribution.lo src/ims/isotopedistribution.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF src/ims/.deps/isotopedistribution.Tpo -c src/ims/isotopedistribution.cpp -fPIC -DPIC -o src/ims/.libs/isotopedistribution.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF src/ims/.deps/isotopedistribution.Tpo -c src/ims/isotopedistribution.cpp -o src/ims/isotopedistribution.o >/dev/null 2>&1
depbase=`echo src/ims/alphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/alphabet.lo src/ims/alphabet.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF src/ims/.deps/alphabet.Tpo -c src/ims/alphabet.cpp -fPIC -DPIC -o src/ims/.libs/alphabet.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF src/ims/.deps/alphabet.Tpo -c src/ims/alphabet.cpp -o src/ims/alphabet.o >/dev/null 2>&1
depbase=`echo src/ims/weights.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/weights.lo src/ims/weights.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF src/ims/.deps/weights.Tpo -c src/ims/weights.cpp -fPIC -DPIC -o src/ims/.libs/weights.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF src/ims/.deps/weights.Tpo -c src/ims/weights.cpp -o src/ims/weights.o >/dev/null 2>&1
depbase=`echo src/ims/distributedalphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/distributedalphabet.lo src/ims/distributedalphabet.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF src/ims/.deps/distributedalphabet.Tpo -c src/ims/distributedalphabet.cpp -fPIC -DPIC -o src/ims/.libs/distributedalphabet.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF src/ims/.deps/distributedalphabet.Tpo -c src/ims/distributedalphabet.cpp -o src/ims/distributedalphabet.o >/dev/null 2>&1
depbase=`echo src/ims/transformation.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/transformation.lo src/ims/transformation.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF src/ims/.deps/transformation.Tpo -c src/ims/transformation.cpp -fPIC -DPIC -o src/ims/.libs/transformation.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF src/ims/.deps/transformation.Tpo -c src/ims/transformation.cpp -o src/ims/transformation.o >/dev/null 2>&1
depbase=`echo src/ims/isotopespecies.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/isotopespecies.lo src/ims/isotopespecies.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF src/ims/.deps/isotopespecies.Tpo -c src/ims/isotopespecies.cpp -fPIC -DPIC -o src/ims/.libs/isotopespecies.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF src/ims/.deps/isotopespecies.Tpo -c src/ims/isotopespecies.cpp -o src/ims/isotopespecies.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/alphabettextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/alphabettextparser.lo src/ims/base/parser/alphabettextparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/base/parser/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/alphabettextparser.Tpo -c src/ims/base/parser/alphabettextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/alphabettextparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/alphabettextparser.Tpo -c src/ims/base/parser/alphabettextparser.cpp -o src/ims/base/parser/alphabettextparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/distributedalphabettextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/distributedalphabettextparser.lo src/ims/base/parser/distributedalphabettextparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/distributedalphabettextparser.Tpo -c src/ims/base/parser/distributedalphabettextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/distributedalphabettextparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/distributedalphabettextparser.Tpo -c src/ims/base/parser/distributedalphabettextparser.cpp -o src/ims/base/parser/distributedalphabettextparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/massestextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/massestextparser.lo src/ims/base/parser/massestextparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF src/ims/base/parser/.deps/massestextparser.Tpo -c src/ims/base/parser/massestextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/massestextparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF src/ims/base/parser/.deps/massestextparser.Tpo -c src/ims/base/parser/massestextparser.cpp -o src/ims/base/parser/massestextparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/moleculesequenceparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/moleculesequenceparser.lo src/ims/base/parser/moleculesequenceparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculesequenceparser.Tpo -c src/ims/base/parser/moleculesequenceparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/moleculesequenceparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculesequenceparser.Tpo -c src/ims/base/parser/moleculesequenceparser.cpp -o src/ims/base/parser/moleculesequenceparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/standardmoleculesequenceparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/standardmoleculesequenceparser.lo src/ims/base/parser/standardmoleculesequenceparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/standardmoleculesequenceparser.Tpo -c src/ims/base/parser/standardmoleculesequenceparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/standardmoleculesequenceparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/standardmoleculesequenceparser.Tpo -c src/ims/base/parser/standardmoleculesequenceparser.cpp -o src/ims/base/parser/standardmoleculesequenceparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/keggligandcompoundsparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/keggligandcompoundsparser.lo src/ims/base/parser/keggligandcompoundsparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF src/ims/base/parser/.deps/keggligandcompoundsparser.Tpo -c src/ims/base/parser/keggligandcompoundsparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/keggligandcompoundsparser.o
src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const std::string&)':
src/ims/base/parser/keggligandcompoundsparser.cpp:55: warning: suggest parentheses around && within ||
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF src/ims/base/parser/.deps/keggligandcompoundsparser.Tpo -c src/ims/base/parser/keggligandcompoundsparser.cpp -o src/ims/base/parser/keggligandcompoundsparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/moleculeionchargemodificationparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/moleculeionchargemodificationparser.lo src/ims/base/parser/moleculeionchargemodificationparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculeionchargemodificationparser.Tpo -c src/ims/base/parser/moleculeionchargemodificationparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/moleculeionchargemodificationparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculeionchargemodificationparser.Tpo -c src/ims/base/parser/moleculeionchargemodificationparser.cpp -o src/ims/base/parser/moleculeionchargemodificationparser.o >/dev/null 2>&1
depbase=`echo src/ims/calib/linepairstabber.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/calib/linepairstabber.lo src/ims/calib/linepairstabber.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/calib/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF src/ims/calib/.deps/linepairstabber.Tpo -c src/ims/calib/linepairstabber.cpp -fPIC -DPIC -o src/ims/calib/.libs/linepairstabber.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF src/ims/calib/.deps/linepairstabber.Tpo -c src/ims/calib/linepairstabber.cpp -o src/ims/calib/linepairstabber.o >/dev/null 2>&1
depbase=`echo src/ims/calib/matchmatrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/calib/matchmatrix.lo src/ims/calib/matchmatrix.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -fPIC -DPIC -o src/ims/calib/.libs/matchmatrix.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -o src/ims/calib/matchmatrix.o >/dev/null 2>&1
depbase=`echo src/ims/calib/linearpointsetmatcher.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/calib/linearpointsetmatcher.lo src/ims/calib/linearpointsetmatcher.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -fPIC -DPIC -o src/ims/calib/.libs/linearpointsetmatcher.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -o src/ims/calib/linearpointsetmatcher.o >/dev/null 2>&1
depbase=`echo src/ims/decomp/realmassdecomposer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/decomp/realmassdecomposer.lo src/ims/decomp/realmassdecomposer.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/decomp/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -fPIC -DPIC -o src/ims/decomp/.libs/realmassdecomposer.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -o src/ims/decomp/realmassdecomposer.o >/dev/null 2>&1
depbase=`echo src/ims/utils/distribution.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/utils/distribution.lo src/ims/utils/distribution.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/utils/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -fPIC -DPIC -o src/ims/utils/.libs/distribution.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -o src/ims/utils/distribution.o >/dev/null 2>&1
depbase=`echo src/ims/distributionprobabilityscorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/distributionprobabilityscorer.lo src/ims/distributionprobabilityscorer.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -fPIC -DPIC -o src/ims/.libs/distributionprobabilityscorer.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -o src/ims/distributionprobabilityscorer.o >/dev/null 2>&1
depbase=`echo src/ims/characteralphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/characteralphabet.lo src/ims/characteralphabet.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -fPIC -DPIC -o src/ims/.libs/characteralphabet.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -o src/ims/characteralphabet.o >/dev/null 2>&1
depbase=`echo src/ims/nitrogenrulefilter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/nitrogenrulefilter.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/nitrogenrulefilter.lo src/ims/nitrogenrulefilter.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/nitrogenrulefilter.lo -MD -MP -MF src/ims/.deps/nitrogenrulefilter.Tpo -c src/ims/nitrogenrulefilter.cpp -fPIC -DPIC -o src/ims/.libs/nitrogenrulefilter.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/nitrogenrulefilter.lo -MD -MP -MF src/ims/.deps/nitrogenrulefilter.Tpo -c src/ims/nitrogenrulefilter.cpp -o src/ims/nitrogenrulefilter.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CXX --mode=link g++ -Wall -W -Wwrite-strings -Wundef -g -O2 -o src/libims.la -rpath /usr/local/lib -no-undefined -version-info 0:0:0 src/ims/element.lo src/ims/composedelement.lo src/ims/isotopedistribution.lo src/ims/alphabet.lo src/ims/weights.lo src/ims/distributedalphabet.lo src/ims/transformation.lo src/ims/isotopespecies.lo src/ims/base/parser/alphabettextparser.lo src/ims/base/parser/distributedalphabettextparser.lo src/ims/base/parser/massestextparser.lo src/ims/base/parser/moleculesequenceparser.lo src/ims/base/parser/standardmoleculesequenceparser.lo src/ims/base/parser/keggligandcompoundsparser.lo src/ims/base/parser/moleculeionchargemodificationparser.lo src/ims/calib/linepairstabber.lo src/ims/calib/matchmatrix.lo src/ims/calib/linearpointsetmatcher.lo src/ims/decomp/realmassdecomposer.lo src/ims/utils/distribution.lo src/ims/distributionprobabilityscorer.lo src/ims/characteralphabet.lo src/ims/nitrogenrulefilter.lo
mkdir src/.libs
g++ -shared -nostdlib /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.3/crtbeginS.o src/ims/.libs/element.o src/ims/.libs/composedelement.o src/ims/.libs/isotopedistribution.o src/ims/.libs/alphabet.o src/ims/.libs/weights.o src/ims/.libs/distributedalphabet.o src/ims/.libs/transformation.o src/ims/.libs/isotopespecies.o src/ims/base/parser/.libs/alphabettextparser.o src/ims/base/parser/.libs/distributedalphabettextparser.o src/ims/base/parser/.libs/massestextparser.o src/ims/base/parser/.libs/moleculesequenceparser.o src/ims/base/parser/.libs/standardmoleculesequenceparser.o src/ims/base/parser/.libs/keggligandcompoundsparser.o src/ims/base/parser/.libs/moleculeionchargemodificationparser.o src/ims/calib/.libs/linepairstabber.o src/ims/calib/.libs/matchmatrix.o src/ims/calib/.libs/linearpointsetmatcher.o src/ims/decomp/.libs/realmassdecomposer.o src/ims/utils/.libs/distribution.o src/ims/.libs/distributionprobabilityscorer.o src/ims/.libs/characteralphabet.o src/ims/.libs/nitrogenrulefilter.o -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib64/gcc/x86_64-suse-linux/4.3/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crtn.o -Wl,-soname -Wl,libims.so.0 -o src/.libs/libims.so.0.0.0
(cd src/.libs && rm -f libims.so.0 && ln -s libims.so.0.0.0 libims.so.0)
(cd src/.libs && rm -f libims.so && ln -s libims.so.0.0.0 libims.so)
ar cru src/.libs/libims.a src/ims/element.o src/ims/composedelement.o src/ims/isotopedistribution.o src/ims/alphabet.o src/ims/weights.o src/ims/distributedalphabet.o src/ims/transformation.o src/ims/isotopespecies.o src/ims/base/parser/alphabettextparser.o src/ims/base/parser/distributedalphabettextparser.o src/ims/base/parser/massestextparser.o src/ims/base/parser/moleculesequenceparser.o src/ims/base/parser/standardmoleculesequenceparser.o src/ims/base/parser/keggligandcompoundsparser.o src/ims/base/parser/moleculeionchargemodificationparser.o src/ims/calib/linepairstabber.o src/ims/calib/matchmatrix.o src/ims/calib/linearpointsetmatcher.o src/ims/decomp/realmassdecomposer.o src/ims/utils/distribution.o src/ims/distributionprobabilityscorer.o src/ims/characteralphabet.o src/ims/nitrogenrulefilter.o
ranlib src/.libs/libims.a
creating src/libims.la
(cd src/.libs && rm -f libims.la && ln -s ../libims.la libims.la)
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.6-bioc/meat/Rdisop.Rcheck/00_pkg_src/Rdisop/src/imslib'
ls -l ./imslib/src/.libs/
total 7940
-rw-r--r-- 1 biocbuild compbio 5732248 2010-10-04 19:25 libims.a
lrwxrwxrwx 1 biocbuild compbio 12 2010-10-04 19:25 libims.la -> ../libims.la
-rw-r--r-- 1 biocbuild compbio 801 2010-10-04 19:25 libims.lai
lrwxrwxrwx 1 biocbuild compbio 15 2010-10-04 19:25 libims.so -> libims.so.0.0.0
lrwxrwxrwx 1 biocbuild compbio 15 2010-10-04 19:25 libims.so.0 -> libims.so.0.0.0
-rwxr-xr-x 1 biocbuild compbio 2374545 2010-10-04 19:25 libims.so.0.0.0
cp -rv ./imslib/src/.libs/*ims*.so* .
`./imslib/src/.libs/libims.so' -> `./libims.so'
`./imslib/src/.libs/libims.so.0' -> `./libims.so.0'
`./imslib/src/.libs/libims.so.0.0.0' -> `./libims.so.0.0.0'
g++ -shared -L/usr/local/lib64 -o Rdisop.so disop.o -L../RcppSrc -lRcpp -L./imslib/src/.libs/ -lims -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/Rdisop.Rcheck/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Rdisop)