Package: Biobase

Version: 2.13.7

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.13.7.tar.gz

StartedAt: 2011-07-06 23:45:26 -0700 (Wed, 06 Jul 2011)

EndedAt: 2011-07-06 23:46:50 -0700 (Wed, 06 Jul 2011)

EllapsedTime: 84.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘2.13.7’
* 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 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
  ‘/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	0.000	0.013
ScalarObject-class	0.064	0.000	0.062
addVig2Menu	0	0	0
anyMissing	0.000	0.000	0.001
biocReposList	0.004	0.004	0.015
cache	0.000	0.000	0.003
channel	0.228	0.000	0.239
channelNames	0.108	0.000	0.110
class.AnnotatedDataFrame	0.052	0.000	0.052
class.ExpressionSet	0.412	0.004	0.418
class.MIAxE	0.028	0.000	0.027
class.MultiSet	0.060	0.004	0.061
class.NChannelSet	0.376	0.008	0.386
class.Versioned	0.116	0.000	0.117
class.VersionedBiobase	0.056	0.000	0.057
class.Versions	0.020	0.000	0.022
class.VersionsNull	0.000	0.004	0.001
class.container	0.004	0.000	0.004
class.eSet	0.188	0.004	0.198
classVersion	0.012	0.000	0.014
combine	0.084	0.000	0.087
contents	0.000	0.004	0.001
copyEnv	0.000	0.000	0.001
copySubstitute	0.008	0.004	0.016
createPackage	0.004	0.008	0.009
data.aaMap	0.004	0.000	0.003
data.geneData	0.028	0.000	0.028
data.reporter	0.004	0.000	0.003
data.sample.ExpressionSet	0.02	0.00	0.02
data.sample.MultiSet	0.000	0.000	0.005
dumpPackTxt	0.004	0.000	0.043
esApply	2.964	0.004	3.034
getPkgVigs	0.032	0.000	0.037
isCurrent	0.080	0.000	0.082
isUnique	0	0	0
isVersioned	0.032	0.000	0.033
lcSuffix	0.004	0.000	0.002
listLen	0.000	0.000	0.001
makeDataPackage	0.084	0.000	0.085
matchpt	0.004	0.000	0.006
multiassign	0.004	0.000	0.000
note	0	0	0
openPDF	0	0	0
openVignette	0	0	0
package.version	0.004	0.000	0.001
read.AnnotatedDataFrame	0.080	0.000	0.082
read.MIAME	0.004	0.000	0.004
readExpressionSet	0.100	0.004	0.106
reverseSplit	0.000	0.000	0.001
rowMedians	0.072	0.000	0.073
rowQ	0.028	0.000	0.028
selectChannels	0.104	0.000	0.103
selectSome	0	0	0
strbreak	0	0	0
subListExtract	1.872	0.036	1.907
testBioCConnection	0.004	0.000	0.010
updateObject	0.216	0.000	0.217
updateOldESet	0	0	0
validMsg	0	0	0