Rdisop 1.13.0
Steffen Neumann
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rdisop | | Last Changed Rev: 54802 / Revision: 55359 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / 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 |
* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/Rdisop.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.13.0’
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘Rdisop’ ...
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-4.2 -arch i386 accepts -g... yes
checking how to run the C++ preprocessor... g++-4.2 -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
checking for a thread-safe mkdir -p... config/install-sh -c -d
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checking whether make sets $(MAKE)... yes
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
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
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checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) is GNU ld... no
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checking the name lister (/usr/bin/nm -p) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld option to reload object files... -r
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checking whether the gcc linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin9.8.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
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checking whether to build static libraries... no
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
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checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
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checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) is GNU ld... no
checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
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checking whether the g++ linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin9.8.0 dyld
checking how to hardcode library paths into programs... immediate
checking for cppunit-config... no
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configure: WARNING: Cppunit not found, make check will not work
checking for round in -lm... yes
checking for floor in -lm... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating libims.pc
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
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$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF src/ims/.deps/element.Tpo -c src/ims/element.cpp -fno-common -DPIC -o src/ims/.libs/element.o
In file included from src/ims/element.cpp:6:
./src/ims/element.h: In member function 'double ims::Element::getMass(size_t) const':
./src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/composedelement.lo | sed 's|[^/]*$|.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/composedelement.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/composedelement.lo src/ims/composedelement.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF src/ims/.deps/composedelement.Tpo -c src/ims/composedelement.cpp -fno-common -DPIC -o src/ims/.libs/composedelement.o
In file included from ./src/ims/composedelement.h:7,
from src/ims/composedelement.cpp:8:
./src/ims/element.h: In member function 'double ims::Element::getMass(size_t) const':
./src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/isotopedistribution.lo | sed 's|[^/]*$|.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/isotopedistribution.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/isotopedistribution.lo src/ims/isotopedistribution.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF src/ims/.deps/isotopedistribution.Tpo -c src/ims/isotopedistribution.cpp -fno-common -DPIC -o src/ims/.libs/isotopedistribution.o
depbase=`echo src/ims/alphabet.lo | sed 's|[^/]*$|.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/alphabet.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/alphabet.lo src/ims/alphabet.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF src/ims/.deps/alphabet.Tpo -c src/ims/alphabet.cpp -fno-common -DPIC -o src/ims/.libs/alphabet.o
In file included from ./src/ims/alphabet.h:8,
from src/ims/alphabet.cpp:6:
./src/ims/element.h: In member function 'double ims::Element::getMass(size_t) const':
./src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/weights.lo | sed 's|[^/]*$|.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/weights.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/weights.lo src/ims/weights.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF src/ims/.deps/weights.Tpo -c src/ims/weights.cpp -fno-common -DPIC -o src/ims/.libs/weights.o
depbase=`echo src/ims/distributedalphabet.lo | sed 's|[^/]*$|.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/distributedalphabet.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/distributedalphabet.lo src/ims/distributedalphabet.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF src/ims/.deps/distributedalphabet.Tpo -c src/ims/distributedalphabet.cpp -fno-common -DPIC -o src/ims/.libs/distributedalphabet.o
In file included from ./src/ims/alphabet.h:8,
from ./src/ims/distributedalphabet.h:7,
from src/ims/distributedalphabet.cpp:7:
./src/ims/element.h: In member function 'double ims::Element::getMass(size_t) const':
./src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/transformation.lo | sed 's|[^/]*$|.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/transformation.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/transformation.lo src/ims/transformation.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF src/ims/.deps/transformation.Tpo -c src/ims/transformation.cpp -fno-common -DPIC -o src/ims/.libs/transformation.o
depbase=`echo src/ims/isotopespecies.lo | sed 's|[^/]*$|.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/isotopespecies.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/isotopespecies.lo src/ims/isotopespecies.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF src/ims/.deps/isotopespecies.Tpo -c src/ims/isotopespecies.cpp -fno-common -DPIC -o src/ims/.libs/isotopespecies.o
depbase=`echo src/ims/base/parser/alphabettextparser.lo | sed 's|[^/]*$|.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/base/parser/alphabettextparser.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/base/parser/alphabettextparser.lo src/ims/base/parser/alphabettextparser.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/alphabettextparser.Tpo -c src/ims/base/parser/alphabettextparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/alphabettextparser.o
depbase=`echo src/ims/base/parser/distributedalphabettextparser.lo | sed 's|[^/]*$|.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/base/parser/distributedalphabettextparser.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/base/parser/distributedalphabettextparser.lo src/ims/base/parser/distributedalphabettextparser.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/distributedalphabettextparser.Tpo -c src/ims/base/parser/distributedalphabettextparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/distributedalphabettextparser.o
depbase=`echo src/ims/base/parser/massestextparser.lo | sed 's|[^/]*$|.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/base/parser/massestextparser.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/base/parser/massestextparser.lo src/ims/base/parser/massestextparser.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF src/ims/base/parser/.deps/massestextparser.Tpo -c src/ims/base/parser/massestextparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/massestextparser.o
depbase=`echo src/ims/base/parser/moleculesequenceparser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/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 &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculesequenceparser.Tpo -c src/ims/base/parser/moleculesequenceparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/moleculesequenceparser.o
depbase=`echo src/ims/base/parser/standardmoleculesequenceparser.lo | sed 's|[^/]*$|.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/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/base/parser/standardmoleculesequenceparser.lo src/ims/base/parser/standardmoleculesequenceparser.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/standardmoleculesequenceparser.Tpo -c src/ims/base/parser/standardmoleculesequenceparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/standardmoleculesequenceparser.o
depbase=`echo src/ims/base/parser/keggligandcompoundsparser.lo | sed 's|[^/]*$|.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/base/parser/keggligandcompoundsparser.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/base/parser/keggligandcompoundsparser.lo src/ims/base/parser/keggligandcompoundsparser.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF src/ims/base/parser/.deps/keggligandcompoundsparser.Tpo -c src/ims/base/parser/keggligandcompoundsparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/keggligandcompoundsparser.o
depbase=`echo src/ims/base/parser/moleculeionchargemodificationparser.lo | sed 's|[^/]*$|.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/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF $depbase.Tpo -c -o src/ims/base/parser/moleculeionchargemodificationparser.lo src/ims/base/parser/moleculeionchargemodificationparser.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculeionchargemodificationparser.Tpo -c src/ims/base/parser/moleculeionchargemodificationparser.cpp -fno-common -DPIC -o src/ims/base/parser/.libs/moleculeionchargemodificationparser.o
depbase=`echo src/ims/calib/linepairstabber.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -fno-common -DPIC -o src/ims/decomp/.libs/realmassdecomposer.o
In file included from ./src/ims/alphabet.h:8,
from ./src/ims/decomp/decomputils.h:12,
from src/ims/decomp/realmassdecomposer.cpp:9:
./src/ims/element.h: In member function 'double ims::Element::getMass(size_t) const':
./src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/utils/distribution.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -fno-common -DPIC -o src/ims/.libs/characteralphabet.o
In file included from ./src/ims/alphabet.h:8,
from ./src/ims/characteralphabet.h:6,
from src/ims/characteralphabet.cpp:3:
./src/ims/element.h: In member function 'double ims::Element::getMass(size_t) const':
./src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/nitrogenrulefilter.lo | sed 's|[^/]*$|.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
In file included from ./src/ims/composedelement.h:7,
from ./src/ims/nitrogenrulefilter.h:4,
from src/ims/nitrogenrulefilter.cpp:5:
./src/ims/element.h: In member function 'double ims::Element::getMass(size_t) const':
./src/ims/element.h:166: warning: comparison between signed and unsigned integer expressions
/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c disop.cpp -o disop.o
disop.cpp: In function ‘void initializeAlphabet(SEXPREC*, alphabet_t&, int)’:
disop.cpp:797: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:799: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:801: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:803: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:804: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:805: warning: deprecated conversion from string constant to ‘char*’
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fPIC -g -O2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
g++-4.2 -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-2.9-bioc/meat/Rdisop.Rcheck/Rdisop/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘Rdisop.Rnw’
** testing if installed package can be loaded
* DONE (Rdisop)