BioC 3.3: CHECK report for Biobase on linux2.bioconductor.org

Package: Biobase

Version: 2.31.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.31.0.tar.gz

StartedAt: 2015-10-27 02:00:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:01:32 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 73.6 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.31.0’
* 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 ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... OK
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [17s/17s]
  Running ‘test-rowMedians.R’ [18s/18s]
 [35s/35s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.006	0.000	0.006
ScalarObject-class	0.008	0.000	0.008
addVig2Menu	0.001	0.000	0.001
anyMissing	0.001	0.000	0.002
cache	0.003	0.000	0.003
channel	0.079	0.000	0.078
channelNames	0.04	0.00	0.04
class.AnnotatedDataFrame	0.022	0.000	0.021
class.ExpressionSet	0.155	0.004	0.159
class.MIAxE	0.014	0.000	0.014
class.MultiSet	0.022	0.000	0.022
class.NChannelSet	0.122	0.000	0.122
class.Versioned	0.04	0.00	0.04
class.VersionedBiobase	0.018	0.004	0.022
class.Versions	0.011	0.000	0.011
class.VersionsNull	0.001	0.000	0.001
class.container	0.003	0.000	0.002
class.eSet	0.065	0.000	0.064
classVersion	0.003	0.000	0.003
contents	0.001	0.000	0.001
copyEnv	0.001	0.000	0.000
copySubstitute	0.008	0.000	0.008
createPackage	0.000	0.004	0.005
data.aaMap	0.002	0.000	0.002
data.geneData	0.066	0.000	0.066
data.reporter	0.001	0.000	0.001
data.sample.ExpressionSet	0.011	0.000	0.011
data.sample.MultiSet	0.005	0.000	0.004
dumpPackTxt	0.002	0.000	0.008
esApply	0.986	0.000	0.986
getPkgVigs	0.003	0.004	0.014
isCurrent	0.027	0.000	0.027
isUnique	0.001	0.000	0.000
isVersioned	0.009	0.000	0.009
lcSuffix	0.002	0.000	0.002
listLen	0.001	0.000	0.000
makeDataPackage	0.057	0.000	0.057
matchpt	0.004	0.000	0.004
multiassign	0.001	0.000	0.001
note	0.000	0.000	0.001
openPDF	0.001	0.000	0.001
openVignette	0.001	0.000	0.000
package.version	0.001	0.004	0.001
read.AnnotatedDataFrame	0.007	0.000	0.010
read.MIAME	0.002	0.000	0.002
readExpressionSet	0.045	0.000	0.045
reverseSplit	0.000	0.000	0.001
rowMedians	0.083	0.000	0.085
rowQ	0.015	0.000	0.015
selectChannels	0.036	0.000	0.037
selectSome	0.001	0.000	0.000
strbreak	0.001	0.000	0.001
subListExtract	0.679	0.008	0.686
testBioCConnection	0.008	0.000	0.032
updateOldESet	0	0	0
validMsg	0	0	0