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GeneR

2.4.0

Y. d'Aubenton-Carafa
Last Changed Date: 2006-10-03 12:16:03 -0700
Last Changed Rev: 20373
lamb1 Linux (SUSE 10.1) x86_64  OK [ OK ]
wellington Linux (SUSE 9.2) i686  OK  OK 
churchill Solaris 2.9 sparc  OK  OK 
lemming Windows Server 2003 x86_64  OK  OK  OK 
Package: GeneR
Version: 2.4.0
Command: /home/biocbuild/bbs-1.9/R/bin/R CMD check GeneR_2.4.0.tar.gz
RetCode: 0
Time: 27.9 seconds
Status: OK
CheckDir: GeneR.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-1.9/meat/GeneR.Rcheck'
* using R version 2.4.1 (2006-12-18)
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.4.0'
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... 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 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating GeneR-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneR-manual.tex ... OK
* checking GeneR-manual.tex ... OK

GeneR.Rcheck/00install.out:

* Installing *source* package 'GeneR' ...
** libs
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c complementaire.cc -o complementaire.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c compoSeq.cc -o compoSeq.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c dnaRna.cc -o dnaRna.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c GeneR_glob.cc -o GeneR_glob.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c GeneR_seq.cc -o GeneR_seq.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c libIndex.cc -o libIndex.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c libStrings.cc -o libStrings.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c makeIndex.cc -o makeIndex.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c masked.cc -o masked.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/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-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readEmblDescript.cc -o readEmblDescript.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readIndex.cc -o readIndex.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readLocation.cc -o readLocation.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readSeqFasta.cc -o readSeqFasta.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readSeqGbk.cc -o readSeqGbk.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c seqManip.cc -o seqManip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c strcasestr.c -o strcasestr.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c translate.cc -o translate.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c upperSeq.cc -o upperSeq.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c vecteurs.cc -o vecteurs.o
g++ -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/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 complementaire.o compoSeq.o dnaRna.o GeneR_glob.o GeneR_seq.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   
** R
** demo
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'GeneR'
     Formats: text html latex example 
  01GeneR                           text    html    latex   example
  02globalSeg                       text    html    latex   example
  02globals                         text    html    latex   example
  Allorf                            text    html    latex   example
  AtoR                              text    html    latex   example
  Match                             text    html    latex   example
  Xor.globalSeg                     text    html    latex   example
  Xor.segSet                        text    html    latex   example
  and.globalSeg                     text    html    latex   example
  and.segSet                        text    html    latex   example
  appendSeq                         text    html    latex   example
  as.globalSeg                      text    html    latex
  as.segSet                         text    html    latex
  assemble                          text    html    latex   example
  bankDensityProfile                text    html    latex   example
  bankSummary                       text    html    latex   example
  compos.seq                        text    html    latex   example
  concat                            text    html    latex   example
  deleteCR                          text    html    latex   example
  densityProfile                    text    html    latex   example
  dna.rna                           text    html    latex   example
  exact.word                        text    html    latex   example
  fasta.descript                    text    html    latex   example
  free.seq                          text    html    latex   example
  getAccn                           text    html    latex
  getParam                          text    html    latex
  getseq                            text    html    latex   example
  indexfasta                        text    html    latex
  insert                            text    html    latex   example
  lower                             text    html    latex   example
  makeIndex                         text    html    latex   example
  mask                              text    html    latex   example
  not.globalSeg                     text    html    latex   example
  not.segSet                        text    html    latex   example
  or.globalSeg                      text    html    latex   example
  or.segSet                         text    html    latex   example
  placestring                       text    html    latex   example
  plot.globalSeg                    text    html    latex   example
  posMaskedSeq                      text    html    latex   example
  randomSeq                         text    html    latex   example
  read.gbk.location                 text    html    latex   example
  readEmblDescript                  text    html    latex   example
  readseq                           text    html    latex   example
  relist                            text    html    latex   example
  revcomp                           text    html    latex   example
  seqSkew                           text    html    latex   example
  sequrl                            text    html    latex   example
  setAccn                           text    html    latex
  setParam                          text    html    latex
  size.globalSeg                    text    html    latex   example
  sizeseq                           text    html    latex   example
  sizeseqfasta                      text    html    latex   example
  sliceSegment                      text    html    latex   example
  translation                       text    html    latex   example
  write.fasta                       text    html    latex   example
  writeEMBL                         text    html    latex   example
** building package indices ...
* DONE (GeneR)