Package: Biobase

Version: 2.11.9

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.11.9.tar.gz

StartedAt: 2011-02-24 18:10:05 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:11:24 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 78.6 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/Biobase.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘2.11.9’
* 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 ... 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-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-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	0.008	0.000	0.010
ScalarObject-class	0.06	0.00	0.06
addVig2Menu	0	0	0
anyMissing	0.000	0.000	0.001
biocReposList	0	0	0
cache	0.004	0.000	0.002
channel	0.244	0.000	0.245
channelNames	0.052	0.000	0.052
class.AnnotatedDataFrame	0.048	0.000	0.049
class.ExpressionSet	0.388	0.004	0.391
class.MIAxE	0.028	0.000	0.026
class.MultiSet	0.064	0.000	0.063
class.NChannelSet	0.348	0.000	0.349
class.Versioned	0.108	0.000	0.110
class.VersionedBiobase	0.052	0.004	0.054
class.Versions	0.024	0.000	0.022
class.VersionsNull	0.000	0.000	0.001
class.container	0.004	0.000	0.004
class.eSet	0.184	0.000	0.182
classVersion	0.012	0.000	0.012
combine	0.088	0.000	0.088
contents	0.000	0.000	0.002
copyEnv	0.000	0.000	0.001
copySubstitute	0.012	0.000	0.010
createPackage	0.008	0.000	0.008
data.aaMap	0.004	0.000	0.002
data.geneData	0.032	0.000	0.031
data.reporter	0.000	0.000	0.001
data.sample.ExpressionSet	0.020	0.000	0.017
data.sample.MultiSet	0.004	0.000	0.004
dumpPackTxt	0.000	0.000	0.055
esApply	2.912	0.016	2.960
getPkgVigs	0.024	0.020	0.044
isCurrent	0.076	0.004	0.080
isUnique	0	0	0
isVersioned	0.032	0.000	0.034
lcSuffix	0.000	0.004	0.002
listLen	0	0	0
makeDataPackage	0.076	0.004	0.079
matchpt	0.012	0.000	0.010
multiassign	0.000	0.000	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0.000	0.000	0.001
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.020	0.000	0.017
read.MIAME	0.004	0.000	0.005
readExpressionSet	0.116	0.004	0.118
reverseSplit	0.000	0.000	0.001
rowMedians	0.124	0.004	0.129
rowQ	0.016	0.004	0.025
selectChannels	0.096	0.000	0.095
selectSome	0	0	0
strbreak	0	0	0
subListExtract	2.004	0.024	2.033
testBioCConnection	0.008	0.000	0.012
updateObject	0.216	0.004	0.228
updateOldESet	0	0	0
validMsg	0	0	0