Rdisop 1.2.0
Steffen Neumann
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/Rdisop | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | 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 (10.5.6) / i386 | N O T S U P P O R T E D |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/Rdisop.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'Rdisop/DESCRIPTION' ... OK
* this is package 'Rdisop' version '1.2.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Rdisop' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
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* checking R code for possible problems ... OK
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* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating Rdisop-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating Rdisop-manual.tex ... OK
* checking Rdisop-manual.tex using pdflatex ... OK
* Installing *source* package 'Rdisop' ...
checking for C++ compiler default output file name... a.out
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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
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configure: creating libtool
appending configuration tag "CXX" to libtool
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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
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checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
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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
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checking for Cppunit - version >= 1.8.0... configure: WARNING: Cppunit not found, make check will not work
checking for round in -lm... yes
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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
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-2.3-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-2.3-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-2.3-bioc/meat/Rdisop.Rcheck/00_pkg_src/Rdisop/src/imslib'
depbase=`echo src/ims/element.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/element.lo src/ims/element.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF src/ims/.deps/element.Tpo -c src/ims/element.cpp -fPIC -DPIC -o src/ims/.libs/element.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF src/ims/.deps/element.Tpo -c src/ims/element.cpp -o src/ims/element.o >/dev/null 2>&1
depbase=`echo src/ims/composedelement.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/composedelement.lo src/ims/composedelement.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF src/ims/.deps/composedelement.Tpo -c src/ims/composedelement.cpp -fPIC -DPIC -o src/ims/.libs/composedelement.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF src/ims/.deps/composedelement.Tpo -c src/ims/composedelement.cpp -o src/ims/composedelement.o >/dev/null 2>&1
depbase=`echo src/ims/isotopedistribution.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/isotopedistribution.lo src/ims/isotopedistribution.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF src/ims/.deps/isotopedistribution.Tpo -c src/ims/isotopedistribution.cpp -fPIC -DPIC -o src/ims/.libs/isotopedistribution.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF src/ims/.deps/isotopedistribution.Tpo -c src/ims/isotopedistribution.cpp -o src/ims/isotopedistribution.o >/dev/null 2>&1
depbase=`echo src/ims/alphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/alphabet.lo src/ims/alphabet.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF src/ims/.deps/alphabet.Tpo -c src/ims/alphabet.cpp -fPIC -DPIC -o src/ims/.libs/alphabet.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF src/ims/.deps/alphabet.Tpo -c src/ims/alphabet.cpp -o src/ims/alphabet.o >/dev/null 2>&1
depbase=`echo src/ims/weights.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/weights.lo src/ims/weights.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF src/ims/.deps/weights.Tpo -c src/ims/weights.cpp -fPIC -DPIC -o src/ims/.libs/weights.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF src/ims/.deps/weights.Tpo -c src/ims/weights.cpp -o src/ims/weights.o >/dev/null 2>&1
depbase=`echo src/ims/distributedalphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/distributedalphabet.lo src/ims/distributedalphabet.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF src/ims/.deps/distributedalphabet.Tpo -c src/ims/distributedalphabet.cpp -fPIC -DPIC -o src/ims/.libs/distributedalphabet.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF src/ims/.deps/distributedalphabet.Tpo -c src/ims/distributedalphabet.cpp -o src/ims/distributedalphabet.o >/dev/null 2>&1
depbase=`echo src/ims/transformation.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/transformation.lo src/ims/transformation.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF src/ims/.deps/transformation.Tpo -c src/ims/transformation.cpp -fPIC -DPIC -o src/ims/.libs/transformation.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF src/ims/.deps/transformation.Tpo -c src/ims/transformation.cpp -o src/ims/transformation.o >/dev/null 2>&1
depbase=`echo src/ims/isotopespecies.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/isotopespecies.lo src/ims/isotopespecies.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF src/ims/.deps/isotopespecies.Tpo -c src/ims/isotopespecies.cpp -fPIC -DPIC -o src/ims/.libs/isotopespecies.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF src/ims/.deps/isotopespecies.Tpo -c src/ims/isotopespecies.cpp -o src/ims/isotopespecies.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/alphabettextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/alphabettextparser.lo src/ims/base/parser/alphabettextparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/base/parser/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/alphabettextparser.Tpo -c src/ims/base/parser/alphabettextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/alphabettextparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/alphabettextparser.Tpo -c src/ims/base/parser/alphabettextparser.cpp -o src/ims/base/parser/alphabettextparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/distributedalphabettextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/distributedalphabettextparser.lo src/ims/base/parser/distributedalphabettextparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/distributedalphabettextparser.Tpo -c src/ims/base/parser/distributedalphabettextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/distributedalphabettextparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/distributedalphabettextparser.Tpo -c src/ims/base/parser/distributedalphabettextparser.cpp -o src/ims/base/parser/distributedalphabettextparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/massestextparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/massestextparser.lo src/ims/base/parser/massestextparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF src/ims/base/parser/.deps/massestextparser.Tpo -c src/ims/base/parser/massestextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/massestextparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF src/ims/base/parser/.deps/massestextparser.Tpo -c src/ims/base/parser/massestextparser.cpp -o src/ims/base/parser/massestextparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/moleculesequenceparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/moleculesequenceparser.lo src/ims/base/parser/moleculesequenceparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculesequenceparser.Tpo -c src/ims/base/parser/moleculesequenceparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/moleculesequenceparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculesequenceparser.Tpo -c src/ims/base/parser/moleculesequenceparser.cpp -o src/ims/base/parser/moleculesequenceparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/standardmoleculesequenceparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/standardmoleculesequenceparser.lo src/ims/base/parser/standardmoleculesequenceparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/standardmoleculesequenceparser.Tpo -c src/ims/base/parser/standardmoleculesequenceparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/standardmoleculesequenceparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/standardmoleculesequenceparser.Tpo -c src/ims/base/parser/standardmoleculesequenceparser.cpp -o src/ims/base/parser/standardmoleculesequenceparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/keggligandcompoundsparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/keggligandcompoundsparser.lo src/ims/base/parser/keggligandcompoundsparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF src/ims/base/parser/.deps/keggligandcompoundsparser.Tpo -c src/ims/base/parser/keggligandcompoundsparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/keggligandcompoundsparser.o
src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const std::string&)':
src/ims/base/parser/keggligandcompoundsparser.cpp:55: warning: suggest parentheses around && within ||
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF src/ims/base/parser/.deps/keggligandcompoundsparser.Tpo -c src/ims/base/parser/keggligandcompoundsparser.cpp -o src/ims/base/parser/keggligandcompoundsparser.o >/dev/null 2>&1
depbase=`echo src/ims/base/parser/moleculeionchargemodificationparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/base/parser/moleculeionchargemodificationparser.lo src/ims/base/parser/moleculeionchargemodificationparser.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculeionchargemodificationparser.Tpo -c src/ims/base/parser/moleculeionchargemodificationparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/moleculeionchargemodificationparser.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculeionchargemodificationparser.Tpo -c src/ims/base/parser/moleculeionchargemodificationparser.cpp -o src/ims/base/parser/moleculeionchargemodificationparser.o >/dev/null 2>&1
depbase=`echo src/ims/calib/linepairstabber.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/calib/linepairstabber.lo src/ims/calib/linepairstabber.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/calib/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF src/ims/calib/.deps/linepairstabber.Tpo -c src/ims/calib/linepairstabber.cpp -fPIC -DPIC -o src/ims/calib/.libs/linepairstabber.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF src/ims/calib/.deps/linepairstabber.Tpo -c src/ims/calib/linepairstabber.cpp -o src/ims/calib/linepairstabber.o >/dev/null 2>&1
depbase=`echo src/ims/calib/matchmatrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/calib/matchmatrix.lo src/ims/calib/matchmatrix.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -fPIC -DPIC -o src/ims/calib/.libs/matchmatrix.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -o src/ims/calib/matchmatrix.o >/dev/null 2>&1
depbase=`echo src/ims/calib/linearpointsetmatcher.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/calib/linearpointsetmatcher.lo src/ims/calib/linearpointsetmatcher.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -fPIC -DPIC -o src/ims/calib/.libs/linearpointsetmatcher.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -o src/ims/calib/linearpointsetmatcher.o >/dev/null 2>&1
depbase=`echo src/ims/decomp/realmassdecomposer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/decomp/realmassdecomposer.lo src/ims/decomp/realmassdecomposer.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/decomp/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -fPIC -DPIC -o src/ims/decomp/.libs/realmassdecomposer.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -o src/ims/decomp/realmassdecomposer.o >/dev/null 2>&1
depbase=`echo src/ims/utils/distribution.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/utils/distribution.lo src/ims/utils/distribution.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
mkdir src/ims/utils/.libs
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -fPIC -DPIC -o src/ims/utils/.libs/distribution.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -o src/ims/utils/distribution.o >/dev/null 2>&1
depbase=`echo src/ims/distributionprobabilityscorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/distributionprobabilityscorer.lo src/ims/distributionprobabilityscorer.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -fPIC -DPIC -o src/ims/.libs/distributionprobabilityscorer.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -o src/ims/distributionprobabilityscorer.o >/dev/null 2>&1
depbase=`echo src/ims/characteralphabet.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/characteralphabet.lo src/ims/characteralphabet.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -fPIC -DPIC -o src/ims/.libs/characteralphabet.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -o src/ims/characteralphabet.o >/dev/null 2>&1
depbase=`echo src/ims/nitrogenrulefilter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/nitrogenrulefilter.lo -MD -MP -MF "$depbase.Tpo" -c -o src/ims/nitrogenrulefilter.lo src/ims/nitrogenrulefilter.cpp; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo"; exit 1; fi
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/nitrogenrulefilter.lo -MD -MP -MF src/ims/.deps/nitrogenrulefilter.Tpo -c src/ims/nitrogenrulefilter.cpp -fPIC -DPIC -o src/ims/.libs/nitrogenrulefilter.o
g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/nitrogenrulefilter.lo -MD -MP -MF src/ims/.deps/nitrogenrulefilter.Tpo -c src/ims/nitrogenrulefilter.cpp -o src/ims/nitrogenrulefilter.o >/dev/null 2>&1
/bin/sh ./libtool --tag=CXX --mode=link g++ -Wall -W -Wwrite-strings -Wundef -g -O2 -o src/libims.la -rpath /usr/local/lib -no-undefined -version-info 0:0:0 src/ims/element.lo src/ims/composedelement.lo src/ims/isotopedistribution.lo src/ims/alphabet.lo src/ims/weights.lo src/ims/distributedalphabet.lo src/ims/transformation.lo src/ims/isotopespecies.lo src/ims/base/parser/alphabettextparser.lo src/ims/base/parser/distributedalphabettextparser.lo src/ims/base/parser/massestextparser.lo src/ims/base/parser/moleculesequenceparser.lo src/ims/base/parser/standardmoleculesequenceparser.lo src/ims/base/parser/keggligandcompoundsparser.lo src/ims/base/parser/moleculeionchargemodificationparser.lo src/ims/calib/linepairstabber.lo src/ims/calib/matchmatrix.lo src/ims/calib/linearpointsetmatcher.lo src/ims/decomp/realmassdecomposer.lo src/ims/utils/distribution.lo src/ims/distributionprobabilityscorer.lo src/ims/characteralphabet.lo src/ims/nitrogenrulefilter.lo
mkdir src/.libs
g++ -shared -nostdlib /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.3/crtbeginS.o src/ims/.libs/element.o src/ims/.libs/composedelement.o src/ims/.libs/isotopedistribution.o src/ims/.libs/alphabet.o src/ims/.libs/weights.o src/ims/.libs/distributedalphabet.o src/ims/.libs/transformation.o src/ims/.libs/isotopespecies.o src/ims/base/parser/.libs/alphabettextparser.o src/ims/base/parser/.libs/distributedalphabettextparser.o src/ims/base/parser/.libs/massestextparser.o src/ims/base/parser/.libs/moleculesequenceparser.o src/ims/base/parser/.libs/standardmoleculesequenceparser.o src/ims/base/parser/.libs/keggligandcompoundsparser.o src/ims/base/parser/.libs/moleculeionchargemodificationparser.o src/ims/calib/.libs/linepairstabber.o src/ims/calib/.libs/matchmatrix.o src/ims/calib/.libs/linearpointsetmatcher.o src/ims/decomp/.libs/realmassdecomposer.o src/ims/utils/.libs/distribution.o src/ims/.libs/distributionprobabilityscorer.o src/ims/.libs/characteralphabet.o src/ims/.libs/nitrogenrulefilter.o -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.3/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib64/gcc/x86_64-suse-linux/4.3/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crtn.o -Wl,-soname -Wl,libims.so.0 -o src/.libs/libims.so.0.0.0
(cd src/.libs && rm -f libims.so.0 && ln -s libims.so.0.0.0 libims.so.0)
(cd src/.libs && rm -f libims.so && ln -s libims.so.0.0.0 libims.so)
ar cru src/.libs/libims.a src/ims/element.o src/ims/composedelement.o src/ims/isotopedistribution.o src/ims/alphabet.o src/ims/weights.o src/ims/distributedalphabet.o src/ims/transformation.o src/ims/isotopespecies.o src/ims/base/parser/alphabettextparser.o src/ims/base/parser/distributedalphabettextparser.o src/ims/base/parser/massestextparser.o src/ims/base/parser/moleculesequenceparser.o src/ims/base/parser/standardmoleculesequenceparser.o src/ims/base/parser/keggligandcompoundsparser.o src/ims/base/parser/moleculeionchargemodificationparser.o src/ims/calib/linepairstabber.o src/ims/calib/matchmatrix.o src/ims/calib/linearpointsetmatcher.o src/ims/decomp/realmassdecomposer.o src/ims/utils/distribution.o src/ims/distributionprobabilityscorer.o src/ims/characteralphabet.o src/ims/nitrogenrulefilter.o
ranlib src/.libs/libims.a
creating src/libims.la
(cd src/.libs && rm -f libims.la && ln -s ../libims.la libims.la)
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.3-bioc/meat/Rdisop.Rcheck/00_pkg_src/Rdisop/src/imslib'
ls -l ./imslib/src/.libs/
total 7940
-rw-r--r-- 1 biocbuild compbio 5732248 2009-04-18 16:27 libims.a
lrwxrwxrwx 1 biocbuild compbio 12 2009-04-18 16:27 libims.la -> ../libims.la
-rw-r--r-- 1 biocbuild compbio 801 2009-04-18 16:27 libims.lai
lrwxrwxrwx 1 biocbuild compbio 15 2009-04-18 16:27 libims.so -> libims.so.0.0.0
lrwxrwxrwx 1 biocbuild compbio 15 2009-04-18 16:27 libims.so.0 -> libims.so.0.0.0
-rwxr-xr-x 1 biocbuild compbio 2374545 2009-04-18 16:27 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-2.3-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
** help
>>> 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)