Rdisop 1.10.0
Steffen Neumann
| Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Rdisop | | Last Changed Rev: 50293 / Revision: 54281 | | Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=Rdisop.buildbin-libdir Rdisop_1.10.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rdisop’ ...
rm -f tools/scoredecompositions tools/peaklistvalidation tools/numberdecompositions tools/keggruntimes tools/imsfrag tools/imsdecomp tools/imsintdecomp tools/histogram tools/decompvalidation tools/imsdecompstatic tools/elementalcompositions
test -z "src/libims.la" || rm -f src/libims.la
rm -f "src/so_locations"
rm -rf .libs _libs
rm -rf examples/.libs examples/_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 -rf tests/.libs tests/_libs
rm -rf tools/.libs tools/_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
rm: src/*.dll: No such file or directory
rm: src/Makedeps: No such file or directory
rm: src/*_res.*: No such file or directory
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
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checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -arch i386 accepts -g... yes
checking how to run the C++ preprocessor... g++ -arch i386 -E
Configuring libims.a in imslib...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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configure: WARNING: Cppunit not found, make check will not work
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configure: creating ./config.status
config.status: creating Makefile
config.status: creating libims.pc
config.status: creating config.h
config.status: config.h is unchanged
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config.status: executing headercreation commands
config.status: creating src/ims/utils/math.h
imslib configuration:
Compiler: g++
Linker: /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld
Compiler flags: -Wall -W -Wwrite-strings -Wundef -g -O2
Preprocessor flags:
Linker flags:
CppUnit available: no
depbase=`echo src/ims/element.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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depbase=`echo src/ims/weights.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: 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 src/ims/.deps/element.Tpo -c src/ims/element.cpp -fno-common -DPIC -o src/ims/.libs/element.o
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libtool: 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 src/ims/.deps/alphabet.Tpo -c src/ims/alphabet.cpp -fno-common -DPIC -o src/ims/.libs/alphabet.o
libtool: 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 src/ims/.deps/isotopedistribution.Tpo -c src/ims/isotopedistribution.cpp -fno-common -DPIC -o src/ims/.libs/isotopedistribution.o
libtool: 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 src/ims/.deps/distributedalphabet.Tpo -c src/ims/distributedalphabet.cpp -fno-common -DPIC -o src/ims/.libs/distributedalphabet.o
libtool: 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 src/ims/.deps/weights.Tpo -c src/ims/weights.cpp -fno-common -DPIC -o src/ims/.libs/weights.o
depbase=`echo src/ims/transformation.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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depbase=`echo src/ims/isotopespecies.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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depbase=`echo src/ims/base/parser/alphabettextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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depbase=`echo src/ims/base/parser/distributedalphabettextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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depbase=`echo src/ims/base/parser/massestextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: 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 src/ims/base/parser/.deps/massestextparser.Tpo -c src/ims/base/parser/massestextparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/massestextparser.o
depbase=`echo src/ims/base/parser/moleculesequenceparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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depbase=`echo src/ims/base/parser/standardmoleculesequenceparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF src/ims/base/parser/.deps/keggligandcompoundsparser.Tpo -c src/ims/base/parser/keggligandcompoundsparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/keggligandcompoundsparser.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculeionchargemodificationparser.Tpo -c src/ims/base/parser/moleculeionchargemodificationparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/moleculeionchargemodificationparser.o
depbase=`echo src/ims/calib/linepairstabber.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF src/ims/calib/.deps/linepairstabber.Tpo -c src/ims/calib/linepairstabber.cpp -fno-common -DPIC -o src/ims/calib/.libs/linepairstabber.o
depbase=`echo src/ims/calib/matchmatrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -fno-common -DPIC -o src/ims/calib/.libs/matchmatrix.o
depbase=`echo src/ims/calib/linearpointsetmatcher.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -fno-common -DPIC -o src/ims/calib/.libs/linearpointsetmatcher.o
depbase=`echo src/ims/decomp/realmassdecomposer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -fno-common -DPIC -o src/ims/decomp/.libs/realmassdecomposer.o
depbase=`echo src/ims/utils/distribution.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -fno-common -DPIC -o src/ims/utils/.libs/distribution.o
depbase=`echo src/ims/distributionprobabilityscorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -fno-common -DPIC -o src/ims/.libs/distributionprobabilityscorer.o
depbase=`echo src/ims/characteralphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -fno-common -DPIC -o src/ims/.libs/characteralphabet.o
depbase=`echo src/ims/nitrogenrulefilter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: 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 src/ims/.deps/nitrogenrulefilter.Tpo -c src/ims/nitrogenrulefilter.cpp -fno-common -DPIC -o src/ims/.libs/nitrogenrulefilter.o
/bin/sh ./libtool --tag=CXX --mode=link g++ -Wall -W -Wwrite-strings -Wundef -g -O2 -no-undefined -version-info 0:0:0 -o src/libims.la -rpath /usr/local/lib 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
libtool: link: g++ -dynamiclib -o src/.libs/libims.0.dylib 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 -install_name /usr/local/lib/libims.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module
libtool: link: dsymutil src/.libs/libims.0.dylib || :
libtool: link: (cd "src/.libs" && rm -f "libims.dylib" && ln -s "libims.0.dylib" "libims.dylib")
libtool: link: ( cd "src/.libs" && rm -f "libims.la" && ln -s "../libims.la" "libims.la" )
Building libRcpp.a in RcppSrc...
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c disop.cpp -o disop.o
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:124: warning: unused variable ‘parityeven’
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:211: warning: comparison between signed and unsigned integer expressions
disop.cpp:214: warning: comparison between signed and unsigned integer expressions
disop.cpp:222: warning: comparison between signed and unsigned integer expressions
disop.cpp:222: warning: comparison between signed and unsigned integer expressions
disop.cpp:174: warning: unused variable ‘number_molecules_shown’
disop.cpp: In function ‘SEXPREC* calculateScore(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:357: warning: comparison between signed and unsigned integer expressions
disop.cpp:357: warning: comparison between signed and unsigned integer expressions
disop.cpp:374: warning: comparison between signed and unsigned integer expressions
disop.cpp:377: warning: comparison between signed and unsigned integer expressions
disop.cpp:381: warning: comparison between signed and unsigned integer expressions
disop.cpp:381: warning: comparison between signed and unsigned integer expressions
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*’
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -L../RcppSrc -lRcpp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Rdisop)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rdisop.buildbin-libdir/Rdisop/libs/i386/Rdisop.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgcc_s.1.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/i386/Rdisop.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/i386/Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/i386/Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/i386/Rdisop.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=Rdisop.buildbin-libdir --libs-only Rdisop_1.10.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rdisop’ ...
rm -f tools/scoredecompositions tools/peaklistvalidation tools/numberdecompositions tools/keggruntimes tools/imsfrag tools/imsdecomp tools/imsintdecomp tools/histogram tools/decompvalidation tools/imsdecompstatic tools/elementalcompositions
test -z "src/libims.la" || rm -f src/libims.la
rm -f "src/so_locations"
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rm -f *.lo
rm: src/*.dll: No such file or directory
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checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
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checking whether g++ -arch ppc accepts -g... yes
checking how to run the C++ preprocessor... g++ -arch ppc -E
Configuring libims.a in imslib...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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checking for gawk... awk
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checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
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checking how to run the C preprocessor... gcc -E
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checking if gcc supports -fno-rtti -fno-exceptions... no
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checking dynamic linker characteristics... darwin9.8.0 dyld
checking how to hardcode library paths into programs... immediate
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checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
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checking dependency style of g++... gcc3
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
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checking dynamic linker characteristics... darwin9.8.0 dyld
checking how to hardcode library paths into programs... immediate
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configure: creating ./config.status
config.status: creating Makefile
config.status: creating libims.pc
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config.status: config.h is unchanged
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config.status: creating src/ims/utils/math.h
imslib configuration:
Compiler: g++
Linker: /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld
Compiler flags: -Wall -W -Wwrite-strings -Wundef -g -O2
Preprocessor flags:
Linker flags:
CppUnit available: no
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/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF src/ims/calib/.deps/linepairstabber.Tpo -c src/ims/calib/linepairstabber.cpp -fno-common -DPIC -o src/ims/calib/.libs/linepairstabber.o
depbase=`echo src/ims/calib/matchmatrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -fno-common -DPIC -o src/ims/calib/.libs/matchmatrix.o
depbase=`echo src/ims/calib/linearpointsetmatcher.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -fno-common -DPIC -o src/ims/calib/.libs/linearpointsetmatcher.o
depbase=`echo src/ims/decomp/realmassdecomposer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -fno-common -DPIC -o src/ims/decomp/.libs/realmassdecomposer.o
depbase=`echo src/ims/utils/distribution.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -fno-common -DPIC -o src/ims/utils/.libs/distribution.o
depbase=`echo src/ims/distributionprobabilityscorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo src/ims/characteralphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -fno-common -DPIC -o src/ims/.libs/distributionprobabilityscorer.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -fno-common -DPIC -o src/ims/.libs/characteralphabet.o
depbase=`echo src/ims/nitrogenrulefilter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: 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 src/ims/.deps/nitrogenrulefilter.Tpo -c src/ims/nitrogenrulefilter.cpp -fno-common -DPIC -o src/ims/.libs/nitrogenrulefilter.o
/bin/sh ./libtool --tag=CXX --mode=link g++ -Wall -W -Wwrite-strings -Wundef -g -O2 -no-undefined -version-info 0:0:0 -o src/libims.la -rpath /usr/local/lib 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
libtool: link: g++ -dynamiclib -o src/.libs/libims.0.dylib 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 -install_name /usr/local/lib/libims.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module
libtool: link: dsymutil src/.libs/libims.0.dylib || :
libtool: link: (cd "src/.libs" && rm -f "libims.dylib" && ln -s "libims.0.dylib" "libims.dylib")
libtool: link: ( cd "src/.libs" && rm -f "libims.la" && ln -s "../libims.la" "libims.la" )
Building libRcpp.a in RcppSrc...
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c disop.cpp -o disop.o
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:124: warning: unused variable ‘parityeven’
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:211: warning: comparison between signed and unsigned integer expressions
disop.cpp:214: warning: comparison between signed and unsigned integer expressions
disop.cpp:222: warning: comparison between signed and unsigned integer expressions
disop.cpp:222: warning: comparison between signed and unsigned integer expressions
disop.cpp:174: warning: unused variable ‘number_molecules_shown’
disop.cpp: In function ‘SEXPREC* calculateScore(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:357: warning: comparison between signed and unsigned integer expressions
disop.cpp:357: warning: comparison between signed and unsigned integer expressions
disop.cpp:374: warning: comparison between signed and unsigned integer expressions
disop.cpp:377: warning: comparison between signed and unsigned integer expressions
disop.cpp:381: warning: comparison between signed and unsigned integer expressions
disop.cpp:381: warning: comparison between signed and unsigned integer expressions
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*’
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -L../RcppSrc -lRcpp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/ppc
* DONE (Rdisop)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rdisop.buildbin-libdir/Rdisop/libs/ppc/Rdisop.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgcc_s.1.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/ppc/Rdisop.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/ppc/Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/ppc/Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/ppc/Rdisop.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=Rdisop.buildbin-libdir --libs-only Rdisop_1.10.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rdisop’ ...
rm -f tools/scoredecompositions tools/peaklistvalidation tools/numberdecompositions tools/keggruntimes tools/imsfrag tools/imsdecomp tools/imsintdecomp tools/histogram tools/decompvalidation tools/imsdecompstatic tools/elementalcompositions
test -z "src/libims.la" || rm -f src/libims.la
rm -f "src/so_locations"
rm -rf .libs _libs
rm -rf examples/.libs examples/_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 -rf tests/.libs tests/_libs
rm -rf tools/.libs tools/_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
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/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -fno-common -DPIC -o src/ims/calib/.libs/linearpointsetmatcher.o
depbase=`echo src/ims/decomp/realmassdecomposer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -fno-common -DPIC -o src/ims/decomp/.libs/realmassdecomposer.o
depbase=`echo src/ims/utils/distribution.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -fno-common -DPIC -o src/ims/utils/.libs/distribution.o
depbase=`echo src/ims/distributionprobabilityscorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo src/ims/characteralphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -fno-common -DPIC -o src/ims/.libs/distributionprobabilityscorer.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -fno-common -DPIC -o src/ims/.libs/characteralphabet.o
depbase=`echo src/ims/nitrogenrulefilter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: 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 src/ims/.deps/nitrogenrulefilter.Tpo -c src/ims/nitrogenrulefilter.cpp -fno-common -DPIC -o src/ims/.libs/nitrogenrulefilter.o
/bin/sh ./libtool --tag=CXX --mode=link g++ -Wall -W -Wwrite-strings -Wundef -g -O2 -no-undefined -version-info 0:0:0 -o src/libims.la -rpath /usr/local/lib 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
libtool: link: g++ -dynamiclib -o src/.libs/libims.0.dylib 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 -install_name /usr/local/lib/libims.0.dylib -compatibility_version 1 -current_version 1.0 -Wl,-single_module
libtool: link: dsymutil src/.libs/libims.0.dylib || :
libtool: link: (cd "src/.libs" && rm -f "libims.dylib" && ln -s "libims.0.dylib" "libims.dylib")
libtool: link: ( cd "src/.libs" && rm -f "libims.la" && ln -s "../libims.la" "libims.la" )
Building libRcpp.a in RcppSrc...
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c disop.cpp -o disop.o
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:124: warning: unused variable ‘parityeven’
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:211: warning: comparison between signed and unsigned integer expressions
disop.cpp:214: warning: comparison between signed and unsigned integer expressions
disop.cpp:222: warning: comparison between signed and unsigned integer expressions
disop.cpp:222: warning: comparison between signed and unsigned integer expressions
disop.cpp:174: warning: unused variable ‘number_molecules_shown’
disop.cpp: In function ‘SEXPREC* calculateScore(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
disop.cpp:357: warning: comparison between signed and unsigned integer expressions
disop.cpp:357: warning: comparison between signed and unsigned integer expressions
disop.cpp:374: warning: comparison between signed and unsigned integer expressions
disop.cpp:377: warning: comparison between signed and unsigned integer expressions
disop.cpp:381: warning: comparison between signed and unsigned integer expressions
disop.cpp:381: warning: comparison between signed and unsigned integer expressions
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*’
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -Wall -fasm-blocks -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -L../RcppSrc -lRcpp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/Rdisop.buildbin-libdir/Rdisop/libs/x86_64
* DONE (Rdisop)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rdisop.buildbin-libdir/Rdisop/libs/x86_64/Rdisop.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgcc_s.1.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/x86_64/Rdisop.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libgfortran.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/x86_64/Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.5.2.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/x86_64/Rdisop.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libreadline.dylib" "Rdisop.buildbin-libdir/Rdisop/libs/x86_64/Rdisop.so"