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Package 80/233HostnameOS / ArchBUILDCHECKBUILD BIN
GeneR 2.8.0
Y. d'Aubenton-Carafa
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/GeneR
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: GeneR
Version: 2.8.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check GeneR_2.8.0.tar.gz
StartedAt: 2008-04-09 19:26:14 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 19:28:28 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 134.0 seconds
RetCode: 0
Status: OK
CheckDir: GeneR.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/GeneR.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.8.0'
* 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 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 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
* 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 R.css in D:/biocbld/bbs-2.1-bioc/meat/GeneR.Rcheck


---------- Making package GeneR ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making strcasestr.d from strcasestr.c
making GeneR_glob.d from GeneR_glob.cc
making GeneR_seq.d from GeneR_seq.cc
making complementaire.d from complementaire.cc
making compoSeq.d from compoSeq.cc
making dnaRna.d from dnaRna.cc
making libIndex.d from libIndex.cc
making libStrings.d from libStrings.cc
making makeIndex.d from makeIndex.cc
making masked.d from masked.cc
making misc.d from misc.cc
making readEmblDescript.d from readEmblDescript.cc
making readIndex.d from readIndex.cc
making readLocation.d from readLocation.cc
making readSeqEmbl.d from readSeqEmbl.cc
making readSeqFasta.d from readSeqFasta.cc
making readSeqGbk.d from readSeqGbk.cc
making seqManip.d from seqManip.cc
making translate.d from translate.cc
making upperSeq.d from upperSeq.cc
making vecteurs.d from vecteurs.cc
making writeFasta.d from writeFasta.cc
gcc-sjlj  -std=gnu99  -Id:/biocbld/bbs-2.1-bioc/R/include     -O3 -Wall  -c strcasestr.c -o strcasestr.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c GeneR_glob.cc -o GeneR_glob.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c GeneR_seq.cc -o GeneR_seq.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c complementaire.cc -o complementaire.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c compoSeq.cc -o compoSeq.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c dnaRna.cc -o dnaRna.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c libIndex.cc -o libIndex.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c libStrings.cc -o libStrings.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c makeIndex.cc -o makeIndex.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c masked.cc -o masked.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c misc.cc -o misc.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c readEmblDescript.cc -o readEmblDescript.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c readIndex.cc -o readIndex.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c readLocation.cc -o readLocation.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c readSeqEmbl.cc -o readSeqEmbl.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c readSeqFasta.cc -o readSeqFasta.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c readSeqGbk.cc -o readSeqGbk.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c seqManip.cc -o seqManip.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c translate.cc -o translate.o
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
translate.cc:35: warning: deprecated conversion from string constant to 'char*'
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c upperSeq.cc -o upperSeq.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c vecteurs.cc -o vecteurs.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c writeFasta.cc -o writeFasta.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include  -i GeneR_res.rc -o GeneR_res.o
g++-sjlj   -shared -s  -o GeneR.dll GeneR.def strcasestr.o 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 translate.o upperSeq.o vecteurs.o writeFasta.o GeneR_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing demos
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'GeneR'
     Formats: text html latex example chm 
  01GeneR                           text    html    latex   example chm
  02globalSeg                       text    html    latex   example chm
  02globals                         text    html    latex   example chm
  Allorf                            text    html    latex   example chm
  AtoR                              text    html    latex   example chm
  Match                             text    html    latex   example chm
  Xor.globalSeg                     text    html    latex   example chm
  Xor.segSet                        text    html    latex   example chm
  and.globalSeg                     text    html    latex   example chm
  and.segSet                        text    html    latex   example chm
  appendSeq                         text    html    latex   example chm
  as.globalSeg                      text    html    latex           chm
  as.segSet                         text    html    latex           chm
  assemble                          text    html    latex   example chm
  bankDensityProfile                text    html    latex   example chm
  bankSummary                       text    html    latex   example chm
  compos.seq                        text    html    latex   example chm
  concat                            text    html    latex   example chm
  deleteCR                          text    html    latex   example chm
  densityProfile                    text    html    latex   example chm
  dna.rna                           text    html    latex   example chm
  exact.word                        text    html    latex   example chm
  fasta.descript                    text    html    latex   example chm
  free.seq                          text    html    latex   example chm
  getAccn                           text    html    latex           chm
  getParam                          text    html    latex           chm
  getseq                            text    html    latex   example chm
  indexfasta                        text    html    latex           chm
  insert                            text    html    latex   example chm
  lower                             text    html    latex   example chm
  makeIndex                         text    html    latex   example chm
  mask                              text    html    latex   example chm
  not.globalSeg                     text    html    latex   example chm
  not.segSet                        text    html    latex   example chm
  or.globalSeg                      text    html    latex   example chm
  or.segSet                         text    html    latex   example chm
  placestring                       text    html    latex   example chm
  plot.globalSeg                    text    html    latex   example chm
  posMaskedSeq                      text    html    latex   example chm
  randomSeq                         text    html    latex   example chm
  read.gbk.location                 text    html    latex   example chm
  readEmblDescript                  text    html    latex   example chm
  readseq                           text    html    latex   example chm
  relist                            text    html    latex   example chm
  revcomp                           text    html    latex   example chm
  seqSkew                           text    html    latex   example chm
  sequrl                            text    html    latex   example chm
  setAccn                           text    html    latex           chm
  setParam                          text    html    latex           chm
  size.globalSeg                    text    html    latex   example chm
  sizeseq                           text    html    latex   example chm
  sizeseqfasta                      text    html    latex   example chm
  sliceSegment                      text    html    latex   example chm
  translation                       text    html    latex   example chm
  write.fasta                       text    html    latex   example chm
  writeEMBL                         text    html    latex   example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.1-bioc\meat\GeneR.Rcheck\00_pkg_src\GeneR\chm\GeneR.chm

HHC4016: Warning: Cannot open "\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".


The following files were not compiled:
  preparing package GeneR for lazy loading
  adding MD5 sums

* DONE (GeneR)