Package: Biobase

Version: 2.18.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.18.0.tar.gz

StartedAt: 2013-03-24 22:42:14 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:44:25 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 131.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Biobase.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '2.18.0'
* 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 ... WARNING
Found the following significant warnings:
  /Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
  /Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
See '/Users/biocbuild/bbs-2.11-bioc/meat/Biobase.Rcheck/00install.out' for details.
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
subListExtract 9.025  0.199   9.301
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R'
  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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-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
In file included from Rinit.c:3:
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
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
In file included from envir.c:5:
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning is a GCC extension
/Library/Frameworks/R.framework/Resources/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0"
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-2.11-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	0.010	0.000	0.011
ScalarObject-class	0.015	0.000	0.015
addVig2Menu	0	0	0
anyMissing	0.001	0.001	0.001
cache	0.004	0.001	0.005
channel	0.192	0.002	0.195
channelNames	0.052	0.001	0.053
class.AnnotatedDataFrame	0.053	0.001	0.053
class.ExpressionSet	0.431	0.012	0.451
class.MIAxE	0.026	0.001	0.027
class.MultiSet	0.051	0.002	0.053
class.NChannelSet	0.265	0.001	0.275
class.Versioned	0.103	0.001	0.104
class.VersionedBiobase	0.047	0.001	0.047
class.Versions	0.018	0.000	0.019
class.VersionsNull	0.001	0.001	0.001
class.container	0.004	0.000	0.004
class.eSet	0.171	0.002	0.174
classVersion	0.011	0.000	0.011
contents	0.001	0.001	0.001
copyEnv	0.001	0.000	0.001
copySubstitute	0.010	0.014	0.025
createPackage	0.011	0.008	0.023
data.aaMap	0.002	0.001	0.003
data.geneData	0.037	0.004	0.042
data.reporter	0.002	0.000	0.003
data.sample.ExpressionSet	0.018	0.004	0.026
data.sample.MultiSet	0.007	0.002	0.008
dumpPackTxt	0.002	0.001	0.081
esApply	2.189	0.016	2.221
getPkgVigs	0.038	0.016	0.062
isCurrent	0.061	0.001	0.064
isUnique	0.000	0.000	0.001
isVersioned	0.026	0.001	0.026
lcSuffix	0.001	0.000	0.002
listLen	0.001	0.001	0.001
makeDataPackage	0.104	0.012	0.119
matchpt	0.006	0.001	0.006
multiassign	0.001	0.000	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0	0	0
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.019	0.004	0.031
read.MIAME	0.005	0.000	0.005
readExpressionSet	0.104	0.008	0.112
reverseSplit	0.000	0.000	0.001
rowMedians	0.153	0.010	0.169
rowQ	0.023	0.008	0.030
selectChannels	0.081	0.001	0.082
selectSome	0.001	0.000	0.001
strbreak	0.002	0.001	0.001
subListExtract	9.025	0.199	9.301
testBioCConnection	0.002	0.001	0.013
updateOldESet	0.000	0.000	0.001
validMsg	0.000	0.000	0.001