BioC 2.12: CHECK report for Biobase on george2

Package: Biobase

Version: 2.20.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.20.1.tar.gz

StartedAt: 2013-10-09 00:24:09 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:27:37 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 207.5 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘2.20.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Biobase’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [30s/32s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
subListExtract 20.069  0.344   21.46
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [45s/46s]
  Running ‘test-rowMedians.R’ [44s/45s]
 [89s/91s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.032	0.004	0.036
ScalarObject-class	0.036	0.004	0.039
addVig2Menu	0.004	0.000	0.006
anyMissing	0.012	0.000	0.010
cache	0.024	0.004	0.027
channel	0.248	0.000	0.247
channelNames	0.068	0.008	0.077
class.AnnotatedDataFrame	0.1	0.0	0.1
class.ExpressionSet	0.496	0.008	0.503
class.MIAxE	0.052	0.000	0.052
class.MultiSet	0.080	0.000	0.079
class.NChannelSet	0.388	0.004	0.392
class.Versioned	0.208	0.004	0.212
class.VersionedBiobase	0.096	0.000	0.095
class.Versions	0.056	0.000	0.056
class.VersionsNull	0.012	0.004	0.017
class.container	0.020	0.000	0.019
class.eSet	0.264	0.020	0.283
classVersion	0.036	0.000	0.037
contents	0.012	0.000	0.014
copyEnv	0.008	0.000	0.010
copySubstitute	0.084	0.008	0.093
createPackage	0.040	0.000	0.037
data.aaMap	0.020	0.000	0.018
data.geneData	0.056	0.004	0.059
data.reporter	0.020	0.000	0.017
data.sample.ExpressionSet	0.032	0.000	0.033
data.sample.MultiSet	0.020	0.000	0.021
dumpPackTxt	0.016	0.000	0.030
esApply	2.616	0.012	2.630
getPkgVigs	0.072	0.008	0.101
isCurrent	0.112	0.004	0.116
isUnique	0.016	0.000	0.016
isVersioned	0.060	0.000	0.078
lcSuffix	0.036	0.000	0.037
listLen	0.012	0.000	0.012
makeDataPackage	0.096	0.000	0.096
matchpt	0.020	0.000	0.027
multiassign	0.016	0.000	0.016
note	0.012	0.000	0.009
openPDF	0.008	0.000	0.007
openVignette	0.008	0.000	0.009
package.version	0.004	0.000	0.007
read.AnnotatedDataFrame	0.040	0.000	0.038
read.MIAME	0.020	0.000	0.019
readExpressionSet	0.140	0.004	0.147
reverseSplit	0.016	0.000	0.016
rowMedians	0.120	0.000	0.129
rowQ	0.044	0.008	0.060
selectChannels	0.128	0.000	0.195
selectSome	0.012	0.000	0.013
strbreak	0.012	0.000	0.011
subListExtract	20.069	0.344	21.460
testBioCConnection	0.008	0.004	0.037
updateOldESet	0.004	0.000	0.020
validMsg	0.012	0.004	0.032