BioC 2.12: CHECK report for Biobase on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘2.19.2’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biobase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
subListExtract 11.089  0.156  11.251
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’
  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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘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	0.016	0.004	0.019
ScalarObject-class	0.024	0.000	0.024
addVig2Menu	0.004	0.004	0.007
anyMissing	0.008	0.000	0.007
cache	0.008	0.008	0.018
channel	0.228	0.000	0.227
channelNames	0.056	0.000	0.056
class.AnnotatedDataFrame	0.084	0.000	0.086
class.ExpressionSet	0.476	0.000	0.478
class.MIAxE	0.060	0.000	0.061
class.MultiSet	0.096	0.004	0.099
class.NChannelSet	0.364	0.000	0.365
class.Versioned	0.132	0.000	0.132
class.VersionedBiobase	0.144	0.000	0.146
class.Versions	0.036	0.000	0.037
class.VersionsNull	0.008	0.000	0.009
class.container	0.012	0.000	0.013
class.eSet	0.184	0.004	0.188
classVersion	0.020	0.000	0.022
contents	0.004	0.000	0.006
copyEnv	0.012	0.000	0.010
copySubstitute	0.044	0.008	0.049
createPackage	0.024	0.000	0.025
data.aaMap	0.008	0.000	0.006
data.geneData	0.032	0.000	0.038
data.reporter	0.020	0.000	0.019
data.sample.ExpressionSet	0.016	0.000	0.019
data.sample.MultiSet	0.012	0.000	0.011
dumpPackTxt	0.008	0.000	0.026
esApply	1.768	0.004	1.774
getPkgVigs	0.028	0.016	0.158
isCurrent	0.144	0.008	0.150
isUnique	0.008	0.000	0.007
isVersioned	0.032	0.000	0.032
lcSuffix	0.020	0.000	0.019
listLen	0.008	0.000	0.007
makeDataPackage	0.084	0.000	0.081
matchpt	0.024	0.000	0.020
multiassign	0.02	0.00	0.02
note	0.008	0.000	0.009
openPDF	0.008	0.000	0.006
openVignette	0.008	0.000	0.007
package.version	0.096	0.000	0.096
read.AnnotatedDataFrame	0.028	0.000	0.028
read.MIAME	0.012	0.000	0.014
readExpressionSet	0.100	0.000	0.103
reverseSplit	0.012	0.000	0.012
rowMedians	0.092	0.000	0.093
rowQ	0.032	0.004	0.035
selectChannels	0.080	0.000	0.082
selectSome	0.008	0.000	0.006
strbreak	0.008	0.000	0.008
subListExtract	11.089	0.156	11.251
testBioCConnection	0.004	0.004	0.017
updateOldESet	0.004	0.000	0.003
validMsg	0.004	0.000	0.005

Summary

Command output