Package: Biobase

Version: 2.19.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.19.3.tar.gz

StartedAt: 2013-03-25 00:17:22 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:20:45 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 202.3 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘2.19.3’
* 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 ... [11s/11s] 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 ... [29s/32s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
subListExtract 18.653   0.32  19.449
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [39s/42s]
  Running ‘test-rowMedians.R’ [42s/43s]
 [82s/85s] 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
  ‘/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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -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  -Wall -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib -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 /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	0.024	0.016	0.042
ScalarObject-class	0.036	0.012	0.050
addVig2Menu	0.008	0.008	0.019
anyMissing	0.028	0.008	0.034
cache	0.020	0.004	0.029
channel	0.272	0.012	0.277
channelNames	0.084	0.004	0.089
class.AnnotatedDataFrame	0.124	0.004	0.130
class.ExpressionSet	0.576	0.016	0.595
class.MIAxE	0.056	0.000	0.054
class.MultiSet	0.084	0.000	0.084
class.NChannelSet	0.576	0.008	0.581
class.Versioned	0.180	0.000	0.179
class.VersionedBiobase	0.088	0.000	0.088
class.Versions	0.048	0.000	0.049
class.VersionsNull	0.016	0.000	0.019
class.container	0.020	0.000	0.019
class.eSet	0.320	0.000	0.356
classVersion	0.044	0.000	0.047
contents	0.016	0.000	0.018
copyEnv	0.008	0.004	0.013
copySubstitute	0.072	0.012	0.096
createPackage	0.032	0.008	0.047
data.aaMap	0.016	0.000	0.014
data.geneData	0.064	0.000	0.065
data.reporter	0.020	0.000	0.019
data.sample.ExpressionSet	0.032	0.000	0.061
data.sample.MultiSet	0.02	0.00	0.02
dumpPackTxt	0.012	0.004	0.035
esApply	3.068	0.024	3.515
getPkgVigs	0.056	0.012	0.793
isCurrent	0.112	0.000	0.115
isUnique	0.012	0.000	0.010
isVersioned	0.052	0.000	0.054
lcSuffix	0.044	0.000	0.042
listLen	0.016	0.000	0.014
makeDataPackage	0.104	0.008	0.112
matchpt	0.036	0.004	0.038
multiassign	0.028	0.000	0.028
note	0.016	0.000	0.015
openPDF	0.008	0.004	0.010
openVignette	0.032	0.000	0.029
package.version	0.012	0.000	0.013
read.AnnotatedDataFrame	0.028	0.004	0.034
read.MIAME	0.020	0.000	0.019
readExpressionSet	0.140	0.000	0.144
reverseSplit	0.236	0.000	0.237
rowMedians	0.120	0.004	0.127
rowQ	0.048	0.000	0.047
selectChannels	0.140	0.000	0.143
selectSome	0.020	0.000	0.033
strbreak	0.024	0.000	0.026
subListExtract	18.653	0.320	19.449
testBioCConnection	0.000	0.008	0.017
updateOldESet	0.004	0.000	0.006
validMsg	0.004	0.000	0.006