rTANDEM 0.99.5
Frederic Fournier
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rTANDEM | | Last Changed Rev: 74013 / Revision: 74774 | | Last Changed Date: 2013-03-07 08:25:48 -0800 (Thu, 07 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/rTANDEM.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rTANDEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rTANDEM’ version ‘0.99.5’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rTANDEM’ can be installed ... [188s/193s] OK
* checking installed package size ... NOTE
installed size is 14.0Mb
sub-directories of 1Mb or more:
extdata 2.9Mb
libs 10.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ‘/home/biocbuild/bbs-2.12-bioc/meat/rTANDEM.Rcheck/rTANDEM/libs/rTANDEM.so’:
Found non-API call to R: ‘R_CStackLimit’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [5s/5s] 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/rTANDEM.Rcheck/00check.log’
for details.
* installing *source* package ‘rTANDEM’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c base64.cpp -o base64.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c dataLoader.cpp -o dataLoader.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c loadmspectrum.cpp -o loadmspectrum.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c masscalc.cpp -o masscalc.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mbiomlreport.cpp -o mbiomlreport.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mpam.cpp -o mpam.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mplugin.cpp -o mplugin.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mpmods.cpp -o mpmods.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mprocess.cpp -o mprocess.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mrefine.cpp -o mrefine.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mreport.cpp -o mreport.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mscore.cpp -o mscore.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mscore_tandem.cpp -o mscore_tandem.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c msequencecollection.cpp -o msequencecollection.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c msequenceserver.cpp -o msequenceserver.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c msequtilities.cpp -o msequtilities.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mspectrumcondition.cpp -o mspectrumcondition.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mtermmods.cpp -o mtermmods.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c mxxcleavage.cpp -o mxxcleavage.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c p3.cpp -o p3.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c p3mprocess.cpp -o p3mprocess.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c p3msequenceserver.cpp -o p3msequenceserver.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxbiomlhandler.cpp -o saxbiomlhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxgamlhandler.cpp -o saxgamlhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxhandler.cpp -o saxhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxmodhandler.cpp -o saxmodhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxmzdatahandler.cpp -o saxmzdatahandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxmzmlhandler.cpp -o saxmzmlhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxmzxmlhandler.cpp -o saxmzxmlhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxsaphandler.cpp -o saxsaphandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxtandeminputhandler.cpp -o saxtandeminputhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c saxtaxhandler.cpp -o saxtaxhandler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c stdafx.cpp -o stdafx.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c tandem.cpp -o tandem.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c xmlparameter.cpp -o xmlparameter.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -fpic -g -O2 -Wall -c xmltaxonomy.cpp -o xmltaxonomy.o
g++ -shared -L/usr/local/lib -o rTANDEM.so base64.o dataLoader.o loadmspectrum.o masscalc.o mbiomlreport.o mpam.o mplugin.o mpmods.o mprocess.o mrefine.o mreport.o mscore.o mscore_tandem.o msequencecollection.o msequenceserver.o msequtilities.o mspectrumcondition.o mtermmods.o mxxcleavage.o p3.o p3mprocess.o p3msequenceserver.o saxbiomlhandler.o saxgamlhandler.o saxhandler.o saxmodhandler.o saxmzdatahandler.o saxmzmlhandler.o saxmzxmlhandler.o saxsaphandler.o saxtandeminputhandler.o saxtaxhandler.o stdafx.o tandem.o xmlparameter.o xmltaxonomy.o -L/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lpthread -lexpat -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/rTANDEM.Rcheck/rTANDEM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘rTANDEM.Rnw’
** testing if installed package can be loaded
* DONE (rTANDEM)