BioC 3.1: CHECK report for Biobase on zin2

Package: Biobase

Version: 2.28.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.28.0.tar.gz

StartedAt: 2015-10-08 22:47:13 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:48:29 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 76.3 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/Biobase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.28.0’
* 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 ... [4s/4s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [18s/18s]
  Running ‘test-rowMedians.R’ [19s/19s]
 [37s/37s] 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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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-3.1-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/home/biocbuild/bbs-3.1-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-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-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	0.007	0.000	0.007
ScalarObject-class	0.012	0.000	0.012
addVig2Menu	0.001	0.000	0.000
anyMissing	0.001	0.000	0.002
cache	0.004	0.000	0.003
channel	0.115	0.000	0.116
channelNames	0.060	0.000	0.064
class.AnnotatedDataFrame	0.032	0.000	0.036
class.ExpressionSet	0.240	0.000	0.244
class.MIAxE	0.016	0.004	0.020
class.MultiSet	0.035	0.000	0.035
class.NChannelSet	0.232	0.000	0.232
class.Versioned	0.06	0.00	0.06
class.VersionedBiobase	0.024	0.000	0.028
class.Versions	0.014	0.000	0.014
class.VersionsNull	0.002	0.000	0.002
class.container	0.004	0.000	0.004
class.eSet	0.094	0.000	0.094
classVersion	0.001	0.004	0.005
contents	0.001	0.000	0.001
copyEnv	0.001	0.000	0.001
copySubstitute	0.011	0.004	0.011
createPackage	0.000	0.004	0.007
data.aaMap	0.002	0.000	0.002
data.geneData	0.021	0.008	0.029
data.reporter	0.001	0.000	0.001
data.sample.ExpressionSet	0.009	0.000	0.013
data.sample.MultiSet	0.001	0.004	0.005
dumpPackTxt	0.002	0.000	0.014
esApply	1.215	0.000	1.214
getPkgVigs	0.009	0.000	0.037
isCurrent	0.032	0.000	0.032
isUnique	0.001	0.000	0.001
isVersioned	0.012	0.000	0.012
lcSuffix	0.002	0.000	0.002
listLen	0.001	0.000	0.001
makeDataPackage	0.06	0.00	0.06
matchpt	0.005	0.000	0.005
multiassign	0.001	0.000	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0.001	0.000	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.008	0.004	0.012
read.MIAME	0.002	0.000	0.002
readExpressionSet	0.111	0.000	0.110
reverseSplit	0.001	0.000	0.001
rowMedians	0.05	0.00	0.05
rowQ	0.014	0.008	0.021
selectChannels	0.049	0.000	0.050
selectSome	0.000	0.004	0.000
strbreak	0.000	0.000	0.002
subListExtract	0.840	0.005	0.843
testBioCConnection	0.010	0.000	0.409
updateOldESet	0	0	0
validMsg	0.001	0.000	0.001