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Package 32/251HostnameOS / ArchBUILDCHECKBUILD BIN
Biobase 1.17.7
Biocore Team c/o BioC user list
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase
Last Changed Rev: 28965 / Revision: 29143
Last Changed Date: 2007-11-29 10:08:27 -0800 (Thu, 29 Nov 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 
Package: Biobase
Version: 1.17.7
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check Biobase_1.17.7.tar.gz
StartedAt: 2007-12-11 03:11:30 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:12:46 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 75.6 seconds
RetCode: 0
Status: OK
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/Biobase.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '1.17.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Biobase' 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
cache: no visible binding for global variable ‘cache_old’
* 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 data for non-ASCII characters ... 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 Biobase-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.2-bioc/meat/Biobase.Rcheck/tests'
  Running 'test-rowMedians.R'
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.2-bioc/meat/Biobase.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './BiobaseDevelopment.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './BiobaseDevelopment.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './Bioconductor.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './Bioconductor.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './esApply.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './esApply.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './ExpressionSetIntroduction.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './ExpressionSetIntroduction.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './HowTo.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './HowTo.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './Qviews.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './Qviews.tex' ...
* creating Biobase-manual.tex ... OK
* checking Biobase-manual.tex ... OK

Biobase.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/Biobase.Rcheck
* Installing *source* package 'Biobase' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so anyMissing.o envir.o matchpt.o Rinit.o rowMedians.o sublist_extract.o   -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: tools
** help
 >>> Building/Updating help pages for package 'Biobase'
     Formats: text html latex example 
  Aggregate                         text    html    latex   example
  Biobase-package                   text    html    latex
  ScalarObject-class                text    html    latex   example
  abstract                          text    html    latex
  addVig2Menu                       text    html    latex   example
  annotatedDataFrameFrom-methods    text    html    latex
  annotation                        text    html    latex
  anyMissing                        text    html    latex   example
  assayData                         text    html    latex
  biocReposList                     text    html    latex   example
  cache                             text    html    latex   example
  channel                           text    html    latex   example
  channelNames                      text    html    latex   example
  class.AnnotatedDataFrame          text    html    latex   example
  class.AssayData                   text    html    latex
  class.ExpressionSet               text    html    latex   example
  class.MIAME                       text    html    latex
  class.MultiSet                    text    html    latex   example
  class.NChannelSet                 text    html    latex   example
  class.SnpSet                      text    html    latex
  class.Versioned                   text    html    latex   example
  class.VersionedBiobase            text    html    latex   example
  class.Versions                    text    html    latex   example
  class.VersionsNull                text    html    latex   example
  class.aggregator                  text    html    latex
  class.annotatedDataset            text    html    latex
  class.characterORmiame            text    html    latex
  class.container                   text    html    latex   example
  class.eSet                        text    html    latex   example
  class.exprList                    text    html    latex
  class.exprMatrix                  text    html    latex
  class.exprSet                     text    html    latex   example
  class.phenoData                   text    html    latex   example
  classVersion                      text    html    latex   example
  combine                           text    html    latex   example
  contents                          text    html    latex   example
  copyEnv                           text    html    latex   example
  copySubstitute                    text    html    latex   example
  createPackage                     text    html    latex   example
  data.aaMap                        text    html    latex   example
  data.eset                         text    html    latex   example
  data.geneData                     text    html    latex   example
  data.reporter                     text    html    latex   example
  data.sample.ExpressionSet         text    html    latex   example
  data.sample.eSet                  text    html    latex   example
  data.sample.exprSet.1             text    html    latex   example
  data.sample.exprSet               text    html    latex   example
  defunct                           text    html    latex
  description                       text    html    latex
  dims                              text    html    latex
  dumpPackTxt                       text    html    latex   example
  esApply                           text    html    latex   example
  exprs                             text    html    latex
  featureData                       text    html    latex
  featureNames                      text    html    latex
  getPkgVigs                        text    html    latex   example
  internals                         text    html    latex
  isCurrent                         text    html    latex   example
  isUnique                          text    html    latex   example
  isVersioned                       text    html    latex   example
  lcSuffix                          text    html    latex   example
  listLen                           text    html    latex   example
  makeDataPackage                   text    html    latex   example
  matchpt                           text    html    latex   example
  multiassign                       text    html    latex   example
  note                              text    html    latex   example
  notes                             text    html    latex
  openPDF                           text    html    latex   example
  openVignette                      text    html    latex   example
  package.version                   text    html    latex   example
  phenoData                         text    html    latex
  read.AnnotatedDataFrame           text    html    latex   example
  read.MIAME                        text    html    latex   example
  read.exprSet                      text    html    latex   example
  read.phenoData                    text    html    latex   example
  readExpressionSet                 text    html    latex   example
  reporterInfo                      text    html    latex
  reverseSplit                      text    html    latex   example
  rowMedians                        text    html    latex   example
  rowQ                              text    html    latex   example
  selectChannels                    text    html    latex   example
  selectSome                        text    html    latex   example
  storageMode                       text    html    latex
  strbreak                          text    html    latex   example
  subListExtract                    text    html    latex   example
  testBioCConnection                text    html    latex   example
  updateObject                      text    html    latex   example
  updateOldESet                     text    html    latex   example
  userQuery                         text    html    latex
  validMsg                          text    html    latex   example
** building package indices ...
Loading required package: methods
* DONE (Biobase)