Package: Biobase

Version: 2.13.6

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.13.6.tar.gz

StartedAt: 2011-06-22 01:42:36 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 01:44:32 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 115.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 2

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* 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 ‘2.13.6’
* 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 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 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 ... WARNING
Undocumented code objects:
  ‘estimateDispersions’ ‘estimateSizeFactors’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: ‘.readRDS’ is deprecated.
  Warning: ‘.readRDS’ is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There were 2 warnings, see
  ‘/Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck/00check.log’
for details

* installing *source* package ‘Biobase’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Rinit.c -o Rinit.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c anyMissing.c -o anyMissing.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c envir.c -o envir.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c matchpt.c -o matchpt.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rowMedians.c -o rowMedians.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c sublist_extract.c -o sublist_extract.o
gcc-4.2 -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	0.042	0.001	0.043
ScalarObject-class	0.030	0.001	0.030
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.002
biocReposList	0.001	0.000	0.000
cache	0.004	0.001	0.006
channel	0.316	0.003	0.321
channelNames	0.081	0.000	0.084
class.AnnotatedDataFrame	0.071	0.001	0.076
class.ExpressionSet	0.590	0.008	0.602
class.MIAxE	0.037	0.001	0.038
class.MultiSet	0.082	0.000	0.082
class.NChannelSet	0.473	0.004	0.484
class.Versioned	0.158	0.001	0.161
class.VersionedBiobase	0.077	0.001	0.078
class.Versions	0.031	0.001	0.031
class.VersionsNull	0.001	0.000	0.002
class.container	0.006	0.000	0.006
class.eSet	0.260	0.002	0.263
classVersion	0.016	0.000	0.016
combine	0.115	0.002	0.116
contents	0.001	0.001	0.002
copyEnv	0.001	0.000	0.001
copySubstitute	0.016	0.008	0.030
createPackage	0.012	0.005	0.025
data.aaMap	0.004	0.001	0.005
data.geneData	0.051	0.003	0.064
data.reporter	0.003	0.000	0.005
data.sample.ExpressionSet	0.040	0.002	0.044
data.sample.MultiSet	0.007	0.000	0.009
dumpPackTxt	0.002	0.001	0.023
esApply	3.817	0.018	3.857
getPkgVigs	0.058	0.007	0.078
isCurrent	0.096	0.001	0.103
isUnique	0.001	0.001	0.001
isVersioned	0.042	0.000	0.043
lcSuffix	0.003	0.000	0.003
listLen	0.001	0.000	0.001
makeDataPackage	0.179	0.009	0.187
matchpt	0.009	0.001	0.009
multiassign	0.001	0.000	0.001
note	0.000	0.000	0.001
openPDF	0	0	0
openVignette	0	0	0
package.version	0.002	0.000	0.001
read.AnnotatedDataFrame	0.022	0.002	0.024
read.MIAME	0.007	0.001	0.007
readExpressionSet	0.138	0.005	0.145
reverseSplit	0.001	0.000	0.001
rowMedians	0.092	0.005	0.096
rowQ	0.045	0.008	0.053
selectChannels	0.133	0.001	0.134
selectSome	0	0	0
strbreak	0.001	0.001	0.002
subListExtract	2.438	0.060	2.516
testBioCConnection	0.002	0.001	0.010
updateObject	0.340	0.004	0.345
updateOldESet	0	0	0
validMsg	0.001	0.000	0.001