Rdisop 1.12.0
Steffen Neumann
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/Rdisop | | Last Changed Rev: 54800 / Revision: 59457 | | Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/Rdisop.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘1.12.0’
* checking package namespace 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 ... NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 6.8Mb
* 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
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* checking R code for possible problems ... OK
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* checking Rd cross-references ... OK
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* 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 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
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Configuring libims.a in imslib...
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./configure: line 14263: syntax error near unexpected token `1.8.0,'
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/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-shared --disable-static --no-create --no-recursion
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./configure: line 14263: syntax error near unexpected token `1.8.0,'
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make: *** [config.status] Error 2
Building libRcpp.a in RcppSrc...
g++ -I/home/biocbuild/bbs-2.8-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-2.8-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:797:26: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:799:86: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:801:47: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:803:23: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:804:55: warning: deprecated conversion from string constant to ‘char*’
disop.cpp:805:65: warning: deprecated conversion from string constant to ‘char*’
g++ -I/home/biocbuild/bbs-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/Rdisop.Rcheck/Rdisop/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Rdisop)