Package: Biobase

Version: 2.19.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.19.3.tar.gz

StartedAt: 2013-03-25 01:22:51 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:25:20 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 149.3 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '2.19.3'
* 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 ... [9s/10s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [16s/16s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
subListExtract 7.369  0.168   7.542
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [30s/30s]
  Running 'test-rowMedians.R' [29s/29s]
 [60s/60s] 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck/00check.log'
for details.

* 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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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 -DNDEBUG  -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-2.12-bioc/meat/Biobase.Rcheck/Biobase/libs/i386
** 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	0.07	0.01	0.08
ScalarObject-class	0.024	0.006	0.029
addVig2Menu	0.008	0.005	0.014
anyMissing	0.007	0.004	0.011
cache	0.016	0.011	0.027
channel	0.208	0.009	0.217
channelNames	0.051	0.005	0.056
class.AnnotatedDataFrame	0.113	0.019	0.132
class.ExpressionSet	0.392	0.031	0.430
class.MIAxE	0.036	0.008	0.044
class.MultiSet	0.055	0.006	0.061
class.NChannelSet	0.285	0.018	0.303
class.Versioned	0.157	0.028	0.186
class.VersionedBiobase	0.066	0.017	0.083
class.Versions	0.035	0.013	0.048
class.VersionsNull	0.009	0.007	0.015
class.container	0.016	0.007	0.024
class.eSet	0.264	0.033	0.298
classVersion	0.020	0.010	0.032
contents	0.007	0.006	0.013
copyEnv	0.007	0.006	0.014
copySubstitute	0.043	0.040	0.084
createPackage	0.023	0.018	0.040
data.aaMap	0.007	0.005	0.013
data.geneData	0.090	0.011	0.102
data.reporter	0.011	0.009	0.021
data.sample.ExpressionSet	0.037	0.009	0.045
data.sample.MultiSet	0.018	0.006	0.024
dumpPackTxt	0.010	0.006	0.037
esApply	2.079	0.035	2.114
getPkgVigs	0.068	0.027	0.120
isCurrent	0.109	0.017	0.125
isUnique	0.011	0.005	0.016
isVersioned	0.050	0.011	0.062
lcSuffix	0.031	0.019	0.050
listLen	0.011	0.005	0.016
makeDataPackage	0.181	0.017	0.198
matchpt	0.025	0.008	0.033
multiassign	0.015	0.008	0.024
note	0.008	0.005	0.011
openPDF	0.061	0.005	0.065
openVignette	0.006	0.005	0.010
package.version	0.007	0.004	0.011
read.AnnotatedDataFrame	0.030	0.011	0.042
read.MIAME	0.012	0.005	0.018
readExpressionSet	0.136	0.014	0.151
reverseSplit	0.009	0.005	0.015
rowMedians	0.114	0.016	0.130
rowQ	0.053	0.015	0.068
selectChannels	0.135	0.008	0.144
selectSome	0.010	0.004	0.014
strbreak	0.010	0.005	0.016
subListExtract	7.369	0.168	7.542
testBioCConnection	0.007	0.007	0.026
updateOldESet	0.005	0.007	0.013
validMsg	0.170	0.009	0.181