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 |
* 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
/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)