GeneR 2.16.0
Y. d'Aubenton-Carafa
| Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/GeneR | | Last Changed Rev: 42684 / Revision: 43539 | | Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.5-bioc/meat/GeneR.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.16.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
and.segSet: possible error in as.segSet(deb, fin): unused argument(s)
(fin)
relist: no visible global function definition for ‘error’
setParam: no visible global function definition for ‘seqSize’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package ‘GeneR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c GeneR_glob.cc -o GeneR_glob.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c GeneR_seq.cc -o GeneR_seq.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c complementaire.cc -o complementaire.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c compoSeq.cc -o compoSeq.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c dnaRna.cc -o dnaRna.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c libIndex.cc -o libIndex.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c libStrings.cc -o libStrings.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c makeIndex.cc -o makeIndex.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c masked.cc -o masked.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c misc.cc -o misc.o
misc.cc: In function ‘SEXPREC* str_to_nbstr(SEXPREC*, SEXPREC*)’:
misc.cc:31: warning: ‘multiple’ may be used uninitialized in this function
misc.cc:30: warning: ‘ans’ may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readEmblDescript.cc -o readEmblDescript.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readIndex.cc -o readIndex.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readLocation.cc -o readLocation.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readSeqFasta.cc -o readSeqFasta.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readSeqGbk.cc -o readSeqGbk.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c seqManip.cc -o seqManip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c strcasestr.c -o strcasestr.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c translate.cc -o translate.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c upperSeq.cc -o upperSeq.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c vecteurs.cc -o vecteurs.o
g++ -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c writeFasta.cc -o writeFasta.o
g++ -shared -L/usr/local/lib64 -o GeneR.so GeneR_glob.o GeneR_seq.o complementaire.o compoSeq.o dnaRna.o libIndex.o libStrings.o makeIndex.o masked.o misc.o readEmblDescript.o readIndex.o readLocation.o readSeqEmbl.o readSeqFasta.o readSeqGbk.o seqManip.o strcasestr.o translate.o upperSeq.o vecteurs.o writeFasta.o -L/home/biocbuild/bbs-2.5-bioc/R/lib -lR
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (GeneR)