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Package 250/319HostnameOS / ArchBUILDCHECKBUILD BIN
Rdisop 1.4.0
Steffen Neumann
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/Rdisop
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64 [ OK ] OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386 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
Package: Rdisop
Version: 1.4.0
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD build Rdisop
StartedAt: 2009-10-20 14:28:31 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 14:29:17 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 45.5 seconds
RetCode: 0
Status: OK
PackageFile: Rdisop_1.4.0.tar.gz
PackageFileSize: 1.914 MiB

Command output

* checking for file 'Rdisop/DESCRIPTION' ... OK
* preparing 'Rdisop':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running cleanup
make: Entering directory `/loc/home/biocbuild/bbs-2.4-bioc/meat/Rdisop/src/imslib'
 rm -f tools/scoredecompositions tools/scoredecompositions
 rm -f tools/peaklistvalidation tools/peaklistvalidation
 rm -f tools/numberdecompositions tools/numberdecompositions
 rm -f tools/keggruntimes tools/keggruntimes
 rm -f tools/imsfrag tools/imsfrag
 rm -f tools/imsdecomp tools/imsdecomp
 rm -f tools/imsintdecomp tools/imsintdecomp
 rm -f tools/histogram tools/histogram
 rm -f tools/decompvalidation tools/decompvalidation
 rm -f tools/imsdecompstatic tools/imsdecompstatic
 rm -f tools/elementalcompositions tools/elementalcompositions
test -z "src/libims.la" || rm -f src/libims.la
rm -f "src/so_locations"
rm -rf .libs _libs
rm -rf src/.libs src/_libs
rm -rf src/ims/.libs src/ims/_libs
rm -rf src/ims/base/parser/.libs src/ims/base/parser/_libs
rm -rf src/ims/calib/.libs src/ims/calib/_libs
rm -rf src/ims/decomp/.libs src/ims/decomp/_libs
rm -rf src/ims/utils/.libs src/ims/utils/_libs
rm -f *.o
rm -f examples/peaklist.o
rm -f src/ims/alphabet.o
rm -f src/ims/alphabet.lo
rm -f src/ims/base/parser/alphabettextparser.o
rm -f src/ims/base/parser/alphabettextparser.lo
rm -f src/ims/base/parser/distributedalphabettextparser.o
rm -f src/ims/base/parser/distributedalphabettextparser.lo
rm -f src/ims/base/parser/keggligandcompoundsparser.o
rm -f src/ims/base/parser/keggligandcompoundsparser.lo
rm -f src/ims/base/parser/massestextparser.o
rm -f src/ims/base/parser/massestextparser.lo
rm -f src/ims/base/parser/moleculeionchargemodificationparser.o
rm -f src/ims/base/parser/moleculeionchargemodificationparser.lo
rm -f src/ims/base/parser/moleculesequenceparser.o
rm -f src/ims/base/parser/moleculesequenceparser.lo
rm -f src/ims/base/parser/standardmoleculesequenceparser.o
rm -f src/ims/base/parser/standardmoleculesequenceparser.lo
rm -f src/ims/calib/linearpointsetmatcher.o
rm -f src/ims/calib/linearpointsetmatcher.lo
rm -f src/ims/calib/linepairstabber.o
rm -f src/ims/calib/linepairstabber.lo
rm -f src/ims/calib/matchmatrix.o
rm -f src/ims/calib/matchmatrix.lo
rm -f src/ims/characteralphabet.o
rm -f src/ims/characteralphabet.lo
rm -f src/ims/composedelement.o
rm -f src/ims/composedelement.lo
rm -f src/ims/decomp/realmassdecomposer.o
rm -f src/ims/decomp/realmassdecomposer.lo
rm -f src/ims/distributedalphabet.o
rm -f src/ims/distributedalphabet.lo
rm -f src/ims/distributionprobabilityscorer.o
rm -f src/ims/distributionprobabilityscorer.lo
rm -f src/ims/element.o
rm -f src/ims/element.lo
rm -f src/ims/isotopedistribution.o
rm -f src/ims/isotopedistribution.lo
rm -f src/ims/isotopespecies.o
rm -f src/ims/isotopespecies.lo
rm -f src/ims/nitrogenrulefilter.o
rm -f src/ims/nitrogenrulefilter.lo
rm -f src/ims/transformation.o
rm -f src/ims/transformation.lo
rm -f src/ims/utils/distribution.o
rm -f src/ims/utils/distribution.lo
rm -f src/ims/weights.o
rm -f src/ims/weights.lo
rm -f tests/alphabettest.o
rm -f tests/base/parser/massestextparsertest.o
rm -f tests/base/parser/moleculesequenceparsertest.o
rm -f tests/calib/linearpointsetmatchertest.o
rm -f tests/calib/linepairstabbertest.o
rm -f tests/calib/matchmatrixtest.o
rm -f tests/chebyshevfittertest.o
rm -f tests/composedelementtest.o
rm -f tests/decomp/integermassdecomposertest.o
rm -f tests/decomp/realmassdecomposertest.o
rm -f tests/decomp/twomassdecomposer2test.o
rm -f tests/distributedalphabettest.o
rm -f tests/distributionprobabilityscorertest.o
rm -f tests/elementtest.o
rm -f tests/exceptiontest.o
rm -f tests/fragmentpeaktest.o
rm -f tests/identitytransformationtest.o
rm -f tests/intensitypeaktest.o
rm -f tests/isotopedistributiontest.o
rm -f tests/isotopespeciestest.o
rm -f tests/lineartransformationtest.o
rm -f tests/markovsequencegeneratortest.o
rm -f tests/massintensitypeaktest.o
rm -f tests/massintensitytofpeaktest.o
rm -f tests/masspeaktest.o
rm -f tests/masstofpeaktest.o
rm -f tests/modifier/intensitynormalizermodifiertest.o
rm -f tests/modifier/massrangemodifiertest.o
rm -f tests/modifier/multimodifiertest.o
rm -f tests/modifier/shiftmodifiertest.o
rm -f tests/modifier/sortmodifiertest.o
rm -f tests/modifier/unificationmodifiertest.o
rm -f tests/modifier/voidmodifiertest.o
rm -f tests/peaklisttest.o
rm -f tests/peakpropertyiteratortest.o
rm -f tests/pmffragmentertest.o
rm -f tests/polynomialtransformationtest.o
rm -f tests/randomsequencegeneratortest.o
rm -f tests/roundtest.o
rm -f tests/shifttransformationtest.o
rm -f tests/stopwatchtest.o
rm -f tests/tests.o
rm -f tests/tofpeaktest.o
rm -f tests/weightstest.o
rm -f tools/decompvalidation.o
rm -f tools/elementalcompositions.o
rm -f tools/histogram.o
rm -f tools/imsdecomp.o
rm -f tools/imsfrag.o
rm -f tools/imsintdecomp.o
rm -f tools/keggruntimes.o
rm -f tools/numberdecompositions.o
rm -f tools/options.o
rm -f tools/peaklistvalidation.o
rm -f tools/scoredecompositions.o
rm -f *.lo
make: Leaving directory `/loc/home/biocbuild/bbs-2.4-bioc/meat/Rdisop/src/imslib'
rm: cannot remove `src/*.dll': No such file or directory
rm: cannot remove `src/Makedeps': No such file or directory
rm: cannot remove `src/*_res.*': No such file or directory
* installing the package to re-build vignettes
* 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
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
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
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... gfortran
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
checking if gcc static flag -static works... yes
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-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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-2.4-bioc/R/include  -I/usr/local/include   -I../RcppSrc -I./imslib/src/ -fpic  -g -O2 -Wall -c disop.cpp -o disop.o
disop.cpp: In function 'bool isValidMyNitrogenRule(const ims::ComposedElement&, int)':
disop.cpp:122: warning: unused variable 'parityeven'
disop.cpp: In function 'SEXPREC* decomposeIsotopes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
disop.cpp:207: warning: comparison between signed and unsigned integer expressions
disop.cpp:210: warning: comparison between signed and unsigned integer expressions
disop.cpp:218: warning: comparison between signed and unsigned integer expressions
disop.cpp:218: warning: comparison between signed and unsigned integer expressions
disop.cpp:171: warning: unused variable 'number_molecules_shown'
disop.cpp: In function 'SEXPREC* calculateScore(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
disop.cpp:353: warning: comparison between signed and unsigned integer expressions
disop.cpp:353: warning: comparison between signed and unsigned integer expressions
disop.cpp:370: warning: comparison between signed and unsigned integer expressions
disop.cpp:373: warning: comparison between signed and unsigned integer expressions
disop.cpp:377: warning: comparison between signed and unsigned integer expressions
disop.cpp:377: warning: comparison between signed and unsigned integer expressions
disop.cpp: In function 'void initializeAlphabet(SEXPREC*, alphabet_t&)':
disop.cpp:789: warning: deprecated conversion from string constant to 'char*'
disop.cpp:791: warning: deprecated conversion from string constant to 'char*'
disop.cpp:793: warning: deprecated conversion from string constant to 'char*'
disop.cpp:795: warning: deprecated conversion from string constant to 'char*'
disop.cpp:796: warning: deprecated conversion from string constant to 'char*'
disop.cpp:797: warning: deprecated conversion from string constant to 'char*'
make -C imslib src/libims.la
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.4-bioc/meat/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|[^/]*$|.deps/&|;s|\.lo$||'`; \
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 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|[^/]*$|.deps/&|;s|\.lo$||'`; \
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 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|[^/]*$|.deps/&|;s|\.lo$||'`; \
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	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$||'`; \
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	then mv -f "$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|[^/]*$|.deps/&|;s|\.lo$||'`; \
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	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$||'`; \
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 g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp  -fPIC -DPIC -o src/ims/calib/.libs/matchmatrix.o
 g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -o src/ims/calib/matchmatrix.o >/dev/null 2>&1
depbase=`echo src/ims/calib/linearpointsetmatcher.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
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	then mv -f "$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|[^/]*$|.deps/&|;s|\.lo$||'`; \
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	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$||'`; \
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	then mv -f "$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|[^/]*$|.deps/&|;s|\.lo$||'`; \
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	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$||'`; \
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	then mv -f "$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|[^/]*$|.deps/&|;s|\.lo$||'`; \
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	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-2.4-bioc/meat/Rdisop/src/imslib'
ls -l ./imslib/src/.libs/
total 7940
-rw-r--r-- 1 biocbuild compbio 5731672 2009-10-20 14:29 libims.a
lrwxrwxrwx 1 biocbuild compbio      12 2009-10-20 14:29 libims.la -> ../libims.la
-rw-r--r-- 1 biocbuild compbio     801 2009-10-20 14:29 libims.lai
lrwxrwxrwx 1 biocbuild compbio      15 2009-10-20 14:29 libims.so -> libims.so.0.0.0
lrwxrwxrwx 1 biocbuild compbio      15 2009-10-20 14:29 libims.so.0 -> libims.so.0.0.0
-rwxr-xr-x 1 biocbuild compbio 2374513 2009-10-20 14:29 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-2.4-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
 >>> Building/Updating help pages for package 'Rdisop'
     Formats: text html latex example 
  RcppVersion                       text    html    latex   example
  addMolecules                      text    html    latex   example
  decomposeMass                     text    html    latex   example
  getMolecule                       text    html    latex   example
  initializeCHNOPS                  text    html    latex   example
** building package indices ...
* DONE (Rdisop)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* running cleanup
make: Entering directory `/loc/home/biocbuild/bbs-2.4-bioc/meat/Rdisop/src/imslib'
 rm -f tools/scoredecompositions tools/scoredecompositions
 rm -f tools/peaklistvalidation tools/peaklistvalidation
 rm -f tools/numberdecompositions tools/numberdecompositions
 rm -f tools/keggruntimes tools/keggruntimes
 rm -f tools/imsfrag tools/imsfrag
 rm -f tools/imsdecomp tools/imsdecomp
 rm -f tools/imsintdecomp tools/imsintdecomp
 rm -f tools/histogram tools/histogram
 rm -f tools/decompvalidation tools/decompvalidation
 rm -f tools/imsdecompstatic tools/imsdecompstatic
 rm -f tools/elementalcompositions tools/elementalcompositions
test -z "src/libims.la" || rm -f src/libims.la
rm -f "src/so_locations"
rm -rf .libs _libs
rm -rf src/.libs src/_libs
rm -rf src/ims/.libs src/ims/_libs
rm -rf src/ims/base/parser/.libs src/ims/base/parser/_libs
rm -rf src/ims/calib/.libs src/ims/calib/_libs
rm -rf src/ims/decomp/.libs src/ims/decomp/_libs
rm -rf src/ims/utils/.libs src/ims/utils/_libs
rm -f *.o
rm -f examples/peaklist.o
rm -f src/ims/alphabet.o
rm -f src/ims/alphabet.lo
rm -f src/ims/base/parser/alphabettextparser.o
rm -f src/ims/base/parser/alphabettextparser.lo
rm -f src/ims/base/parser/distributedalphabettextparser.o
rm -f src/ims/base/parser/distributedalphabettextparser.lo
rm -f src/ims/base/parser/keggligandcompoundsparser.o
rm -f src/ims/base/parser/keggligandcompoundsparser.lo
rm -f src/ims/base/parser/massestextparser.o
rm -f src/ims/base/parser/massestextparser.lo
rm -f src/ims/base/parser/moleculeionchargemodificationparser.o
rm -f src/ims/base/parser/moleculeionchargemodificationparser.lo
rm -f src/ims/base/parser/moleculesequenceparser.o
rm -f src/ims/base/parser/moleculesequenceparser.lo
rm -f src/ims/base/parser/standardmoleculesequenceparser.o
rm -f src/ims/base/parser/standardmoleculesequenceparser.lo
rm -f src/ims/calib/linearpointsetmatcher.o
rm -f src/ims/calib/linearpointsetmatcher.lo
rm -f src/ims/calib/linepairstabber.o
rm -f src/ims/calib/linepairstabber.lo
rm -f src/ims/calib/matchmatrix.o
rm -f src/ims/calib/matchmatrix.lo
rm -f src/ims/characteralphabet.o
rm -f src/ims/characteralphabet.lo
rm -f src/ims/composedelement.o
rm -f src/ims/composedelement.lo
rm -f src/ims/decomp/realmassdecomposer.o
rm -f src/ims/decomp/realmassdecomposer.lo
rm -f src/ims/distributedalphabet.o
rm -f src/ims/distributedalphabet.lo
rm -f src/ims/distributionprobabilityscorer.o
rm -f src/ims/distributionprobabilityscorer.lo
rm -f src/ims/element.o
rm -f src/ims/element.lo
rm -f src/ims/isotopedistribution.o
rm -f src/ims/isotopedistribution.lo
rm -f src/ims/isotopespecies.o
rm -f src/ims/isotopespecies.lo
rm -f src/ims/nitrogenrulefilter.o
rm -f src/ims/nitrogenrulefilter.lo
rm -f src/ims/transformation.o
rm -f src/ims/transformation.lo
rm -f src/ims/utils/distribution.o
rm -f src/ims/utils/distribution.lo
rm -f src/ims/weights.o
rm -f src/ims/weights.lo
rm -f tests/alphabettest.o
rm -f tests/base/parser/massestextparsertest.o
rm -f tests/base/parser/moleculesequenceparsertest.o
rm -f tests/calib/linearpointsetmatchertest.o
rm -f tests/calib/linepairstabbertest.o
rm -f tests/calib/matchmatrixtest.o
rm -f tests/chebyshevfittertest.o
rm -f tests/composedelementtest.o
rm -f tests/decomp/integermassdecomposertest.o
rm -f tests/decomp/realmassdecomposertest.o
rm -f tests/decomp/twomassdecomposer2test.o
rm -f tests/distributedalphabettest.o
rm -f tests/distributionprobabilityscorertest.o
rm -f tests/elementtest.o
rm -f tests/exceptiontest.o
rm -f tests/fragmentpeaktest.o
rm -f tests/identitytransformationtest.o
rm -f tests/intensitypeaktest.o
rm -f tests/isotopedistributiontest.o
rm -f tests/isotopespeciestest.o
rm -f tests/lineartransformationtest.o
rm -f tests/markovsequencegeneratortest.o
rm -f tests/massintensitypeaktest.o
rm -f tests/massintensitytofpeaktest.o
rm -f tests/masspeaktest.o
rm -f tests/masstofpeaktest.o
rm -f tests/modifier/intensitynormalizermodifiertest.o
rm -f tests/modifier/massrangemodifiertest.o
rm -f tests/modifier/multimodifiertest.o
rm -f tests/modifier/shiftmodifiertest.o
rm -f tests/modifier/sortmodifiertest.o
rm -f tests/modifier/unificationmodifiertest.o
rm -f tests/modifier/voidmodifiertest.o
rm -f tests/peaklisttest.o
rm -f tests/peakpropertyiteratortest.o
rm -f tests/pmffragmentertest.o
rm -f tests/polynomialtransformationtest.o
rm -f tests/randomsequencegeneratortest.o
rm -f tests/roundtest.o
rm -f tests/shifttransformationtest.o
rm -f tests/stopwatchtest.o
rm -f tests/tests.o
rm -f tests/tofpeaktest.o
rm -f tests/weightstest.o
rm -f tools/decompvalidation.o
rm -f tools/elementalcompositions.o
rm -f tools/histogram.o
rm -f tools/imsdecomp.o
rm -f tools/imsfrag.o
rm -f tools/imsintdecomp.o
rm -f tools/keggruntimes.o
rm -f tools/numberdecompositions.o
rm -f tools/options.o
rm -f tools/peaklistvalidation.o
rm -f tools/scoredecompositions.o
rm -f *.lo
make: Leaving directory `/loc/home/biocbuild/bbs-2.4-bioc/meat/Rdisop/src/imslib'
rm: cannot remove `src/*.dll': No such file or directory
rm: cannot remove `src/Makedeps': No such file or directory
rm: cannot remove `src/*_res.*': No such file or directory
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'Rdisop_1.4.0.tar.gz'