Rdisop 1.14.0
Steffen Neumann
| Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/Rdisop | | Last Changed Rev: 59920 / Revision: 64395 | | Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | ERROR | ERROR |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Rdisop.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘Rdisop’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
libs 6.5Mb
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Rdisop.Rcheck/Rdisop/libs/Rdisop.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘__assert_fail’, possibly from ‘assert’ (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’
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++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -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... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
checking for gcc... gcc
checking 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
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/x86_64-suse-linux/bin/ld
checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/x86_64-suse-linux/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... failed
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/x86_64-suse-linux/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/x86_64-suse-linux/bin/ld
checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cppunit-config... no
checking for Cppunit - version >= 1.8.0... no
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/x86_64-suse-linux/bin/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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/element.lo -MD -MP -MF src/ims/.deps/element.Tpo -c src/ims/element.cpp -fPIC -DPIC -o src/ims/.libs/element.o
In file included from src/ims/element.cpp:6:0:
./src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./src/ims/element.h:166:46: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/composedelement.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/composedelement.lo -MD -MP -MF src/ims/.deps/composedelement.Tpo -c src/ims/composedelement.cpp -fPIC -DPIC -o src/ims/.libs/composedelement.o
In file included from ./src/ims/composedelement.h:7:0,
from src/ims/composedelement.cpp:8:
./src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./src/ims/element.h:166:46: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/isotopedistribution.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopedistribution.lo -MD -MP -MF src/ims/.deps/isotopedistribution.Tpo -c src/ims/isotopedistribution.cpp -fPIC -DPIC -o src/ims/.libs/isotopedistribution.o
depbase=`echo src/ims/alphabet.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/alphabet.lo -MD -MP -MF src/ims/.deps/alphabet.Tpo -c src/ims/alphabet.cpp -fPIC -DPIC -o src/ims/.libs/alphabet.o
In file included from ./src/ims/alphabet.h:8:0,
from src/ims/alphabet.cpp:6:
./src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./src/ims/element.h:166:46: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/weights.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/weights.lo -MD -MP -MF src/ims/.deps/weights.Tpo -c src/ims/weights.cpp -fPIC -DPIC -o src/ims/.libs/weights.o
depbase=`echo src/ims/distributedalphabet.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributedalphabet.lo -MD -MP -MF src/ims/.deps/distributedalphabet.Tpo -c src/ims/distributedalphabet.cpp -fPIC -DPIC -o src/ims/.libs/distributedalphabet.o
In file included from ./src/ims/alphabet.h:8:0,
from ./src/ims/distributedalphabet.h:7,
from src/ims/distributedalphabet.cpp:7:
./src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./src/ims/element.h:166:46: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/transformation.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/transformation.lo -MD -MP -MF src/ims/.deps/transformation.Tpo -c src/ims/transformation.cpp -fPIC -DPIC -o src/ims/.libs/transformation.o
depbase=`echo src/ims/isotopespecies.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/isotopespecies.lo -MD -MP -MF src/ims/.deps/isotopespecies.Tpo -c src/ims/isotopespecies.cpp -fPIC -DPIC -o src/ims/.libs/isotopespecies.o
depbase=`echo src/ims/base/parser/alphabettextparser.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/alphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/alphabettextparser.Tpo -c src/ims/base/parser/alphabettextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/alphabettextparser.o
depbase=`echo src/ims/base/parser/distributedalphabettextparser.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/distributedalphabettextparser.lo -MD -MP -MF src/ims/base/parser/.deps/distributedalphabettextparser.Tpo -c src/ims/base/parser/distributedalphabettextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/distributedalphabettextparser.o
depbase=`echo src/ims/base/parser/massestextparser.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/massestextparser.lo -MD -MP -MF src/ims/base/parser/.deps/massestextparser.Tpo -c src/ims/base/parser/massestextparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/massestextparser.o
depbase=`echo src/ims/base/parser/moleculesequenceparser.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculesequenceparser.Tpo -c src/ims/base/parser/moleculesequenceparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/moleculesequenceparser.o
depbase=`echo src/ims/base/parser/standardmoleculesequenceparser.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/standardmoleculesequenceparser.lo -MD -MP -MF src/ims/base/parser/.deps/standardmoleculesequenceparser.Tpo -c src/ims/base/parser/standardmoleculesequenceparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/standardmoleculesequenceparser.o
depbase=`echo src/ims/base/parser/keggligandcompoundsparser.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/keggligandcompoundsparser.lo -MD -MP -MF src/ims/base/parser/.deps/keggligandcompoundsparser.Tpo -c src/ims/base/parser/keggligandcompoundsparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/keggligandcompoundsparser.o
src/ims/base/parser/keggligandcompoundsparser.cpp: In member function 'virtual void ims::KeggLigandCompoundsParser::parse(const ims::AbstractMoleculeSequenceParser::sequence_type&)':
src/ims/base/parser/keggligandcompoundsparser.cpp:55:65: warning: suggest parentheses around '&&' within '||'
depbase=`echo src/ims/base/parser/moleculeionchargemodificationparser.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/base/parser/moleculeionchargemodificationparser.lo -MD -MP -MF src/ims/base/parser/.deps/moleculeionchargemodificationparser.Tpo -c src/ims/base/parser/moleculeionchargemodificationparser.cpp -fPIC -DPIC -o src/ims/base/parser/.libs/moleculeionchargemodificationparser.o
depbase=`echo src/ims/calib/linepairstabber.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linepairstabber.lo -MD -MP -MF src/ims/calib/.deps/linepairstabber.Tpo -c src/ims/calib/linepairstabber.cpp -fPIC -DPIC -o src/ims/calib/.libs/linepairstabber.o
depbase=`echo src/ims/calib/matchmatrix.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/matchmatrix.lo -MD -MP -MF src/ims/calib/.deps/matchmatrix.Tpo -c src/ims/calib/matchmatrix.cpp -fPIC -DPIC -o src/ims/calib/.libs/matchmatrix.o
depbase=`echo src/ims/calib/linearpointsetmatcher.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/calib/linearpointsetmatcher.lo -MD -MP -MF src/ims/calib/.deps/linearpointsetmatcher.Tpo -c src/ims/calib/linearpointsetmatcher.cpp -fPIC -DPIC -o src/ims/calib/.libs/linearpointsetmatcher.o
depbase=`echo src/ims/decomp/realmassdecomposer.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/decomp/realmassdecomposer.lo -MD -MP -MF src/ims/decomp/.deps/realmassdecomposer.Tpo -c src/ims/decomp/realmassdecomposer.cpp -fPIC -DPIC -o src/ims/decomp/.libs/realmassdecomposer.o
In file included from ./src/ims/alphabet.h:8:0,
from ./src/ims/decomp/decomputils.h:12,
from src/ims/decomp/realmassdecomposer.cpp:9:
./src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./src/ims/element.h:166:46: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/utils/distribution.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/utils/distribution.lo -MD -MP -MF src/ims/utils/.deps/distribution.Tpo -c src/ims/utils/distribution.cpp -fPIC -DPIC -o src/ims/utils/.libs/distribution.o
depbase=`echo src/ims/distributionprobabilityscorer.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/distributionprobabilityscorer.lo -MD -MP -MF src/ims/.deps/distributionprobabilityscorer.Tpo -c src/ims/distributionprobabilityscorer.cpp -fPIC -DPIC -o src/ims/.libs/distributionprobabilityscorer.o
depbase=`echo src/ims/characteralphabet.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I./src -I./src -Wall -W -Wwrite-strings -Wundef -g -O2 -MT src/ims/characteralphabet.lo -MD -MP -MF src/ims/.deps/characteralphabet.Tpo -c src/ims/characteralphabet.cpp -fPIC -DPIC -o src/ims/.libs/characteralphabet.o
In file included from ./src/ims/alphabet.h:8:0,
from ./src/ims/characteralphabet.h:6,
from src/ims/characteralphabet.cpp:3:
./src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./src/ims/element.h:166:46: warning: comparison between signed and unsigned integer expressions
depbase=`echo src/ims/nitrogenrulefilter.lo | sed 's|[^/]*$|.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 -fPIC -DPIC -o src/ims/.libs/nitrogenrulefilter.o
In file included from ./src/ims/composedelement.h:7:0,
from ./src/ims/nitrogenrulefilter.h:4,
from src/ims/nitrogenrulefilter.cpp:5:
./src/ims/element.h: In member function 'ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const':
./src/ims/element.h:166:46: 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++ -shared -nostdlib /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.5/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/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib64/gcc/x86_64-suse-linux/4.5/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crtn.o -Wl,-soname -Wl,libims.so.0 -o src/.libs/libims.so.0.0.0
libtool: link: (cd "src/.libs" && rm -f "libims.so.0" && ln -s "libims.so.0.0.0" "libims.so.0")
libtool: link: (cd "src/.libs" && rm -f "libims.so" && ln -s "libims.so.0.0.0" "libims.so")
libtool: link: ( cd "src/.libs" && rm -f "libims.la" && ln -s "../libims.la" "libims.la" )
Building libRcpp.a in RcppSrc...
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fpic -g -O2 -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I../RcppSrc -I./imslib/src/ -fpic -g -O2 -c disop.cpp -o disop.o
disop.cpp: In function ‘void initializeAlphabet(SEXPREC*, alphabet_t&, int)’:
disop.cpp:799:26: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:801:86: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:803:47: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:805:23: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:806:55: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:807:65: warning: deprecated conversion from string constant to ‘char*’
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -I/home/biocbuild/bbs-2.9-bioc/R/include -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++ -shared -L/usr/local/lib64 -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 -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/Rdisop.Rcheck/Rdisop/libs
** 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)