Package: Biobase

Version: 2.8.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.8.0.tar.gz

StartedAt: 2010-10-04 16:14:21 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:15:43 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 81.5 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/Biobase.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.8.0'
* 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 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 tests ...
  Running 'test-rowMedians.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'Biobase' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-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-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-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	0.014
ScalarObject-class	0.024	0.000	0.025
addVig2Menu	0.000	0.000	0.001
anyMissing	0.004	0.000	0.001
biocReposList	0	0	0
cache	0.004	0.000	0.004
channel	0.300	0.004	0.301
channelNames	0.072	0.000	0.073
class.AnnotatedDataFrame	0.072	0.000	0.069
class.ExpressionSet	0.548	0.012	0.559
class.MultiSet	0.068	0.000	0.068
class.NChannelSet	0.420	0.000	0.425
class.Versioned	0.144	0.000	0.141
class.VersionedBiobase	0.068	0.000	0.093
class.Versions	0.024	0.000	0.026
class.VersionsNull	0.000	0.004	0.001
class.container	0.004	0.000	0.005
class.eSet	0.232	0.000	0.233
classVersion	0.012	0.000	0.014
combine	0.096	0.000	0.096
contents	0.004	0.000	0.000
copyEnv	0.000	0.000	0.001
copySubstitute	0.008	0.000	0.140
createPackage	0.008	0.000	0.008
data.aaMap	0.004	0.000	0.003
data.geneData	0.028	0.000	0.028
data.reporter	0.000	0.000	0.002
data.sample.ExpressionSet	0.016	0.000	0.018
data.sample.MultiSet	0.004	0.000	0.004
dumpPackTxt	0.000	0.004	0.084
esApply	3.44	0.00	3.44
getPkgVigs	0.040	0.008	0.047
isCurrent	0.108	0.000	0.105
isUnique	0.000	0.000	0.001
isVersioned	0.044	0.000	0.044
lcSuffix	0.000	0.000	0.002
listLen	0.000	0.000	0.001
makeDataPackage	0.084	0.000	0.084
matchpt	0.004	0.000	0.007
multiassign	0	0	0
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	0.022
read.MIAME	0.008	0.000	0.006
readExpressionSet	0.172	0.008	0.181
reverseSplit	0	0	0
rowMedians	0.060	0.004	0.064
rowQ	0.020	0.004	0.025
selectChannels	0.136	0.000	0.135
selectSome	0.000	0.000	0.001
strbreak	0.000	0.000	0.001
subListExtract	2.324	0.032	2.375
testBioCConnection	0.000	0.000	0.008
updateObject	0.308	0.000	0.312
updateOldESet	0	0	0
validMsg	0	0	0