Package: Biobase

Version: 2.10.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.10.0.tar.gz

StartedAt: 2011-03-31 04:37:31 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:38:48 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 77.6 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/Biobase.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘2.10.0’
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-rowMedians.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-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-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.012	0.000	0.010
ScalarObject-class	0.056	0.000	0.056
addVig2Menu	0.000	0.000	0.001
anyMissing	0.004	0.000	0.001
biocReposList	0	0	0
cache	0.004	0.000	0.002
channel	0.228	0.000	0.229
channelNames	0.048	0.000	0.048
class.AnnotatedDataFrame	0.044	0.000	0.046
class.ExpressionSet	0.376	0.004	0.381
class.MultiSet	0.056	0.000	0.057
class.NChannelSet	0.304	0.000	0.303
class.Versioned	0.160	0.004	0.163
class.VersionedBiobase	0.048	0.004	0.051
class.Versions	0.016	0.004	0.020
class.VersionsNull	0.000	0.000	0.001
class.container	0.004	0.004	0.005
class.eSet	0.168	0.000	0.173
classVersion	0.012	0.000	0.009
combine	0.08	0.00	0.08
contents	0.000	0.000	0.001
copyEnv	0.004	0.000	0.001
copySubstitute	0.008	0.000	0.010
createPackage	0.000	0.008	0.008
data.aaMap	0.004	0.000	0.002
data.geneData	0.024	0.004	0.028
data.reporter	0.000	0.000	0.001
data.sample.ExpressionSet	0.016	0.000	0.017
data.sample.MultiSet	0.004	0.000	0.004
dumpPackTxt	0.000	0.000	0.012
esApply	2.684	0.008	2.693
getPkgVigs	0.036	0.000	0.039
isCurrent	0.076	0.000	0.075
isUnique	0.000	0.000	0.001
isVersioned	0.028	0.004	0.032
lcSuffix	0.004	0.000	0.001
listLen	0.000	0.000	0.001
makeDataPackage	0.076	0.000	0.077
matchpt	0.004	0.000	0.005
multiassign	0.000	0.000	0.001
note	0.004	0.000	0.001
openPDF	0	0	0
openVignette	0	0	0
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.02	0.00	0.02
read.MIAME	0.004	0.000	0.004
readExpressionSet	0.152	0.000	0.154
reverseSplit	0.000	0.000	0.001
rowMedians	0.056	0.004	0.060
rowQ	0.024	0.000	0.023
selectChannels	0.088	0.000	0.086
selectSome	0.000	0.000	0.001
strbreak	0.000	0.000	0.001
subListExtract	1.792	0.016	1.805
testBioCConnection	0.000	0.000	0.006
updateObject	0.220	0.000	0.222
updateOldESet	0	0	0
validMsg	0	0	0