Package: Biobase

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.10.0.tar.gz

StartedAt: 2011-03-31 04:45:47 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:47:44 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 116.4 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/Biobase.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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-2.7-bioc/meat/Biobase.Rcheck/Biobase/libs/i386
** 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	0.015	0.001	0.015
ScalarObject-class	0.03	0.00	0.03
addVig2Menu	0.001	0.000	0.001
anyMissing	0.027	0.000	0.027
biocReposList	0.001	0.001	0.001
cache	0.004	0.001	0.005
channel	0.305	0.002	0.308
channelNames	0.073	0.000	0.074
class.AnnotatedDataFrame	0.069	0.001	0.071
class.ExpressionSet	0.562	0.007	0.577
class.MultiSet	0.078	0.000	0.079
class.NChannelSet	0.430	0.002	0.435
class.Versioned	0.212	0.004	0.218
class.VersionedBiobase	0.080	0.001	0.081
class.Versions	0.030	0.001	0.030
class.VersionsNull	0.001	0.001	0.002
class.container	0.006	0.000	0.006
class.eSet	0.264	0.002	0.268
classVersion	0.017	0.000	0.019
combine	0.122	0.002	0.125
contents	0.001	0.001	0.002
copyEnv	0.001	0.000	0.002
copySubstitute	0.016	0.007	0.033
createPackage	0.012	0.004	0.019
data.aaMap	0.004	0.000	0.004
data.geneData	0.050	0.002	0.053
data.reporter	0.003	0.001	0.003
data.sample.ExpressionSet	0.039	0.002	0.042
data.sample.MultiSet	0.008	0.001	0.008
dumpPackTxt	0.002	0.001	0.010
esApply	3.730	0.019	3.784
getPkgVigs	0.054	0.007	0.061
isCurrent	0.103	0.001	0.104
isUnique	0.001	0.001	0.000
isVersioned	0.043	0.000	0.044
lcSuffix	0.003	0.000	0.004
listLen	0.001	0.000	0.001
makeDataPackage	0.157	0.007	0.165
matchpt	0.009	0.000	0.010
multiassign	0.001	0.000	0.001
note	0.001	0.000	0.000
openPDF	0	0	0
openVignette	0.001	0.000	0.001
package.version	0.001	0.000	0.002
read.AnnotatedDataFrame	0.025	0.002	0.027
read.MIAME	0.006	0.000	0.007
readExpressionSet	0.176	0.006	0.192
reverseSplit	0.001	0.000	0.002
rowMedians	0.084	0.008	0.091
rowQ	0.047	0.008	0.054
selectChannels	0.132	0.000	0.138
selectSome	0	0	0
strbreak	0.000	0.000	0.001
subListExtract	2.392	0.058	2.467
testBioCConnection	0.002	0.000	0.010
updateObject	0.339	0.005	0.347
updateOldESet	0.001	0.000	0.001
validMsg	0.000	0.000	0.001