BioC 2.9: CHECK report for Biobase on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘Biobase’ can be installed ... OK
* checking installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-rowMedians.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘BiobaseDevelopment.Rnw’ 
   ‘Bioconductor.Rnw’ 
   ‘ExpressionSetIntroduction.Rnw’ 
   ‘HowTo.Rnw’ 
   ‘Qviews.Rnw’ 
   ‘esApply.Rnw’ 
** testing if installed package can be loaded

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.008	0.000	0.010
ScalarObject-class	0.012	0.000	0.014
addVig2Menu	0.004	0.000	0.001
anyMissing	0.000	0.000	0.002
biocReposList	0.044	0.004	0.077
cache	0.004	0.000	0.003
channel	0.276	0.000	0.279
channelNames	0.032	0.004	0.039
class.AnnotatedDataFrame	0.032	0.004	0.037
class.ExpressionSet	0.272	0.008	0.281
class.MIAxE	0.020	0.000	0.022
class.MultiSet	0.044	0.000	0.041
class.NChannelSet	0.220	0.000	0.219
class.Versioned	0.088	0.000	0.090
class.VersionedBiobase	0.036	0.000	0.039
class.Versions	0.016	0.000	0.018
class.VersionsNull	0.004	0.000	0.001
class.container	0.004	0.000	0.003
class.eSet	0.136	0.000	0.139
classVersion	0.008	0.004	0.009
combine	0.060	0.000	0.062
contents	0.000	0.000	0.001
copyEnv	0	0	0
copySubstitute	0.008	0.000	0.008
createPackage	0.008	0.000	0.008
data.aaMap	0.000	0.000	0.003
data.geneData	0.036	0.000	0.037
data.reporter	0.000	0.004	0.002
data.sample.ExpressionSet	0.020	0.004	0.023
data.sample.MultiSet	0.004	0.000	0.006
dumpPackTxt	0.000	0.004	0.015
esApply	2.192	0.000	2.194
getPkgVigs	0.028	0.008	0.057
isCurrent	0.092	0.000	0.094
isUnique	0.000	0.000	0.001
isVersioned	0.028	0.000	0.027
lcSuffix	0.000	0.000	0.002
listLen	0	0	0
makeDataPackage	0.084	0.004	0.090
matchpt	0.008	0.000	0.009
multiassign	0.004	0.000	0.001
note	0	0	0
openPDF	0.004	0.000	0.001
openVignette	0	0	0
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.028	0.004	0.033
read.MIAME	0.008	0.000	0.008
readExpressionSet	0.148	0.004	0.153
reverseSplit	0.000	0.000	0.001
rowMedians	0.276	0.004	0.280
rowQ	0.024	0.008	0.034
selectChannels	0.112	0.004	0.114
selectSome	0.000	0.000	0.001
strbreak	0.000	0.000	0.001
subListExtract	3.884	0.064	3.984
testBioCConnection	0.004	0.000	0.012
updateObject	0.192	0.000	0.197
updateOldESet	0	0	0
validMsg	0.000	0.000	0.001

Summary

Command output