BioC 3.2: CHECK report for Biobase on zin1

Package: Biobase

Version: 2.30.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.30.0.tar.gz

StartedAt: 2016-04-22 22:28:18 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:29:36 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 77.4 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Biobase.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘2.30.0’
* 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/20s]
 [38s/38s] 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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-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-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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	0.01	0.00	0.01
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.001
cache	0.003	0.000	0.003
channel	0.102	0.000	0.102
channelNames	0.051	0.000	0.051
class.AnnotatedDataFrame	0.027	0.000	0.027
class.ExpressionSet	0.202	0.004	0.212
class.MIAxE	0.018	0.000	0.018
class.MultiSet	0.031	0.000	0.031
class.NChannelSet	0.197	0.004	0.201
class.Versioned	0.052	0.000	0.051
class.VersionedBiobase	0.023	0.000	0.024
class.Versions	0.014	0.000	0.013
class.VersionsNull	0.001	0.000	0.001
class.container	0.002	0.000	0.002
class.eSet	0.076	0.004	0.080
classVersion	0.004	0.000	0.004
contents	0.001	0.000	0.001
copyEnv	0.000	0.000	0.001
copySubstitute	0.011	0.000	0.011
createPackage	0.005	0.000	0.006
data.aaMap	0.000	0.004	0.002
data.geneData	0.023	0.000	0.024
data.reporter	0.002	0.000	0.002
data.sample.ExpressionSet	0.013	0.000	0.012
data.sample.MultiSet	0.001	0.000	0.005
dumpPackTxt	0.000	0.004	0.038
esApply	1.317	0.000	1.317
getPkgVigs	0.010	0.000	0.034
isCurrent	0.035	0.000	0.035
isUnique	0	0	0
isVersioned	0.013	0.000	0.013
lcSuffix	0.003	0.000	0.003
listLen	0.000	0.000	0.001
makeDataPackage	0.059	0.008	0.068
matchpt	0.005	0.000	0.006
multiassign	0.001	0.000	0.001
note	0.001	0.000	0.000
openPDF	0.000	0.000	0.001
openVignette	0	0	0
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.013	0.000	0.013
read.MIAME	0.002	0.000	0.003
readExpressionSet	0.110	0.000	0.109
reverseSplit	0.001	0.000	0.001
rowMedians	0.047	0.000	0.048
rowQ	0.018	0.004	0.022
selectChannels	0.052	0.000	0.051
selectSome	0.000	0.000	0.001
strbreak	0.001	0.000	0.001
subListExtract	0.867	0.000	0.888
testBioCConnection	0.006	0.004	0.419
updateOldESet	0	0	0
validMsg	0.001	0.000	0.000