Package: Biobase

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.14.0.tar.gz

StartedAt: 2012-03-23 23:40:55 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:42:47 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 112.3 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.14.0'
* 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 whether package 'Biobase' can be installed ... OK
* checking installed package size ... 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  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

* installing *source* package 'Biobase' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Rinit.c -o Rinit.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c anyMissing.c -o anyMissing.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c envir.c -o envir.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c matchpt.c -o matchpt.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rowMedians.c -o rowMedians.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c sublist_extract.c -o sublist_extract.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck/Biobase/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   '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	0.017	0.001	0.017
ScalarObject-class	0.021	0.000	0.022
addVig2Menu	0.001	0.000	0.000
anyMissing	0.003	0.000	0.003
biocReposList	0.090	0.010	0.144
cache	0.004	0.001	0.005
channel	0.261	0.003	0.265
channelNames	0.057	0.000	0.057
class.AnnotatedDataFrame	0.053	0.001	0.053
class.ExpressionSet	0.438	0.006	0.445
class.MIAxE	0.032	0.002	0.033
class.MultiSet	0.061	0.001	0.062
class.NChannelSet	0.389	0.004	0.394
class.Versioned	0.128	0.001	0.130
class.VersionedBiobase	0.062	0.001	0.064
class.Versions	0.023	0.001	0.023
class.VersionsNull	0.001	0.001	0.001
class.container	0.004	0.000	0.005
class.eSet	0.207	0.003	0.210
classVersion	0.014	0.001	0.014
combine	0.088	0.003	0.090
contents	0.001	0.001	0.001
copyEnv	0.001	0.000	0.001
copySubstitute	0.011	0.008	0.026
createPackage	0.011	0.006	0.019
data.aaMap	0.003	0.001	0.007
data.geneData	0.046	0.005	0.051
data.reporter	0.002	0.001	0.004
data.sample.ExpressionSet	0.052	0.004	0.058
data.sample.MultiSet	0.011	0.002	0.013
dumpPackTxt	0.002	0.002	0.031
esApply	2.759	0.016	2.792
getPkgVigs	0.047	0.008	0.071
isCurrent	0.076	0.001	0.077
isUnique	0.001	0.000	0.001
isVersioned	0.031	0.000	0.032
lcSuffix	0.002	0.000	0.002
listLen	0.000	0.001	0.001
makeDataPackage	0.179	0.008	0.193
matchpt	0.006	0.000	0.006
multiassign	0.001	0.001	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0.000	0.000	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.016	0.002	0.017
read.MIAME	0.009	0.000	0.009
readExpressionSet	0.125	0.005	0.130
reverseSplit	0.000	0.000	0.001
rowMedians	0.145	0.008	0.154
rowQ	0.058	0.009	0.068
selectChannels	0.107	0.000	0.108
selectSome	0	0	0
strbreak	0.000	0.000	0.001
subListExtract	3.679	0.090	3.807
testBioCConnection	0.002	0.000	0.012
updateObject	0.274	0.006	0.281
updateOldESet	0	0	0
validMsg	0.001	0.000	0.000