Package: Biobase

Version: 2.12.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.12.2.tar.gz

StartedAt: 2011-10-20 13:46:08 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:48:00 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 112.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/Biobase.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '2.12.2'
* checking package namespace 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 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 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-2.8-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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/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-2.8-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	0.016	0.001	0.017
ScalarObject-class	0.029	0.000	0.034
addVig2Menu	0.001	0.000	0.000
anyMissing	0.001	0.000	0.002
biocReposList	0.000	0.000	0.001
cache	0.003	0.001	0.004
channel	0.317	0.001	0.319
channelNames	0.078	0.000	0.078
class.AnnotatedDataFrame	0.099	0.003	0.103
class.ExpressionSet	0.566	0.009	0.576
class.MIAxE	0.035	0.001	0.036
class.MultiSet	0.08	0.00	0.08
class.NChannelSet	0.465	0.004	0.470
class.Versioned	0.157	0.001	0.160
class.VersionedBiobase	0.075	0.001	0.076
class.Versions	0.030	0.001	0.031
class.VersionsNull	0.001	0.000	0.002
class.container	0.005	0.000	0.006
class.eSet	0.254	0.002	0.257
classVersion	0.017	0.000	0.018
combine	0.114	0.003	0.116
contents	0.001	0.000	0.002
copyEnv	0	0	0
copySubstitute	0.013	0.008	0.027
createPackage	0.010	0.005	0.023
data.aaMap	0.004	0.001	0.004
data.geneData	0.041	0.003	0.045
data.reporter	0.003	0.001	0.004
data.sample.ExpressionSet	0.039	0.003	0.042
data.sample.MultiSet	0.007	0.001	0.008
dumpPackTxt	0.002	0.001	0.044
esApply	3.730	0.014	3.773
getPkgVigs	0.056	0.009	0.069
isCurrent	0.102	0.001	0.103
isUnique	0	0	0
isVersioned	0.042	0.000	0.042
lcSuffix	0.002	0.001	0.002
listLen	0.001	0.000	0.001
makeDataPackage	0.159	0.008	0.167
matchpt	0.011	0.001	0.012
multiassign	0.001	0.001	0.001
note	0.000	0.000	0.001
openPDF	0	0	0
openVignette	0.000	0.000	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.021	0.002	0.023
read.MIAME	0.006	0.001	0.006
readExpressionSet	0.189	0.006	0.195
reverseSplit	0.001	0.001	0.001
rowMedians	0.082	0.007	0.091
rowQ	0.048	0.008	0.072
selectChannels	0.133	0.001	0.136
selectSome	0.001	0.000	0.001
strbreak	0.001	0.000	0.000
subListExtract	2.434	0.064	2.521
testBioCConnection	0.002	0.001	0.010
updateObject	0.341	0.006	0.349
updateOldESet	0.000	0.000	0.001
validMsg	0.001	0.000	0.000