Package: Biobase

Version: 2.13.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.13.2.tar.gz

StartedAt: 2011-05-09 13:30:11 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:32:06 -0700 (Mon, 09 May 2011)

EllapsedTime: 115.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘2.13.2’
* 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 ... 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 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 was 1 warning, 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 -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 -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 -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 -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 -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 -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	0.016	0.001	0.016
ScalarObject-class	0.055	0.000	0.056
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.002
biocReposList	0.000	0.001	0.001
cache	0.004	0.001	0.005
channel	0.314	0.004	0.320
channelNames	0.076	0.001	0.076
class.AnnotatedDataFrame	0.069	0.001	0.070
class.ExpressionSet	0.577	0.009	0.592
class.MIAxE	0.037	0.001	0.037
class.MultiSet	0.081	0.001	0.082
class.NChannelSet	0.475	0.005	0.483
class.Versioned	0.160	0.002	0.162
class.VersionedBiobase	0.075	0.001	0.077
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	0.262	0.003	0.265
classVersion	0.016	0.001	0.020
combine	0.116	0.002	0.122
contents	0.001	0.000	0.002
copyEnv	0.000	0.000	0.001
copySubstitute	0.016	0.008	0.037
createPackage	0.011	0.004	0.016
data.aaMap	0.004	0.001	0.009
data.geneData	0.050	0.003	0.063
data.reporter	0.002	0.001	0.003
data.sample.ExpressionSet	0.039	0.002	0.047
data.sample.MultiSet	0.007	0.001	0.008
dumpPackTxt	0.002	0.001	0.021
esApply	3.810	0.015	3.869
getPkgVigs	0.058	0.008	0.079
isCurrent	0.101	0.001	0.103
isUnique	0.000	0.001	0.001
isVersioned	0.039	0.000	0.040
lcSuffix	0.003	0.000	0.003
listLen	0.000	0.001	0.000
makeDataPackage	0.174	0.008	0.182
matchpt	0.009	0.000	0.010
multiassign	0.001	0.000	0.002
note	0.000	0.000	0.001
openPDF	0.000	0.001	0.000
openVignette	0	0	0
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.022	0.002	0.024
read.MIAME	0.007	0.000	0.008
readExpressionSet	0.146	0.006	0.152
reverseSplit	0.001	0.000	0.002
rowMedians	0.092	0.006	0.098
rowQ	0.047	0.009	0.055
selectChannels	0.137	0.001	0.141
selectSome	0.000	0.000	0.002
strbreak	0.001	0.000	0.001
subListExtract	2.426	0.062	2.520
testBioCConnection	0.002	0.001	0.010
updateObject	0.343	0.006	0.352
updateOldESet	0	0	0
validMsg	0.001	0.000	0.000