Package: Biobase

Version: 2.13.2

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.13.2.tar.gz

StartedAt: 2011-05-09 11:41:33 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 11:42:58 -0700 (Mon, 09 May 2011)

EllapsedTime: 84.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-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 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
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck/00check.log’
for details

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck/Biobase/libs
** 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	0.012	0.004	0.014
ScalarObject-class	0.064	0.000	0.065
addVig2Menu	0.000	0.000	0.001
anyMissing	0.000	0.000	0.002
biocReposList	0.004	0.000	0.001
cache	0.000	0.000	0.003
channel	0.260	0.000	0.269
channelNames	0.056	0.000	0.056
class.AnnotatedDataFrame	0.052	0.000	0.055
class.ExpressionSet	0.420	0.016	0.500
class.MIAxE	0.028	0.000	0.032
class.MultiSet	0.064	0.000	0.072
class.NChannelSet	0.400	0.008	0.419
class.Versioned	0.116	0.000	0.128
class.VersionedBiobase	0.056	0.004	0.060
class.Versions	0.020	0.000	0.023
class.VersionsNull	0.000	0.000	0.001
class.container	0.004	0.000	0.005
class.eSet	0.188	0.004	0.198
classVersion	0.008	0.004	0.012
combine	0.084	0.000	0.088
contents	0.000	0.000	0.001
copyEnv	0	0	0
copySubstitute	0.012	0.000	0.011
createPackage	0.012	0.000	0.009
data.aaMap	0.004	0.000	0.003
data.geneData	0.028	0.000	0.031
data.reporter	0.004	0.000	0.002
data.sample.ExpressionSet	0.016	0.000	0.021
data.sample.MultiSet	0.004	0.000	0.004
dumpPackTxt	0.000	0.004	0.021
esApply	3.092	0.016	3.202
getPkgVigs	0.036	0.004	0.048
isCurrent	0.068	0.004	0.070
isUnique	0	0	0
isVersioned	0.032	0.000	0.030
lcSuffix	0.000	0.004	0.002
listLen	0.000	0.000	0.001
makeDataPackage	0.076	0.000	0.081
matchpt	0.008	0.000	0.006
multiassign	0	0	0
note	0	0	0
openPDF	0	0	0
openVignette	0	0	0
package.version	0	0	0
read.AnnotatedDataFrame	0.020	0.000	0.017
read.MIAME	0.004	0.000	0.005
readExpressionSet	0.104	0.004	0.106
reverseSplit	0.000	0.000	0.001
rowMedians	0.072	0.008	0.082
rowQ	0.024	0.004	0.028
selectChannels	0.100	0.000	0.102
selectSome	0.004	0.000	0.001
strbreak	0	0	0
subListExtract	2.060	0.036	2.097
testBioCConnection	0.004	0.000	0.007
updateObject	0.232	0.000	0.234
updateOldESet	0.000	0.000	0.001
validMsg	0.004	0.000	0.001