BioC 3.5: CHECK report for Biobase on malbec2

Package: Biobase

Version: 2.36.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.36.2.tar.gz

StartedAt: 2017-08-15 21:28:40 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:29:52 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 71.3 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.36.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Biobase.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.36.2’
* 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
  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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘Biobase’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sublist_extract.c -o sublist_extract.o
gcc -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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	0.028	0.000	0.029
ScalarObject-class	0.008	0.000	0.009
addVig2Menu	0.000	0.000	0.001
anyMissing	0.000	0.000	0.002
cache	0.004	0.000	0.003
channel	0.272	0.000	0.270
channelNames	0.108	0.000	0.109
class.AnnotatedDataFrame	0.032	0.000	0.031
class.ExpressionSet	0.276	0.000	0.276
class.MIAxE	0.016	0.000	0.014
class.MultiSet	0.02	0.00	0.02
class.NChannelSet	0.136	0.000	0.136
class.Versioned	0.044	0.000	0.041
class.VersionedBiobase	0.016	0.000	0.017
class.Versions	0.008	0.000	0.009
class.VersionsNull	0.000	0.000	0.001
class.container	0.004	0.000	0.002
class.eSet	0.056	0.000	0.059
classVersion	0.004	0.000	0.004
contents	0	0	0
copyEnv	0.016	0.000	0.017
copySubstitute	0.068	0.000	0.071
createPackage	0.004	0.000	0.004
data.aaMap	0.000	0.000	0.002
data.geneData	0.020	0.000	0.023
data.reporter	0.004	0.000	0.001
data.sample.ExpressionSet	0.008	0.004	0.013
data.sample.MultiSet	0.004	0.000	0.005
dumpPackTxt	0.004	0.000	0.023
esApply	0.992	0.000	0.992
getPkgVigs	0.008	0.004	0.028
isCurrent	0.032	0.000	0.035
isUnique	0.000	0.000	0.001
isVersioned	0.012	0.000	0.010
lcSuffix	0.024	0.000	0.023
listLen	0	0	0
makeDataPackage	0.080	0.000	0.081
matchpt	0.016	0.000	0.018
multiassign	0.000	0.000	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0.004	0.000	0.000
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.012	0.000	0.012
read.MIAME	0.032	0.000	0.029
readExpressionSet	0.060	0.000	0.062
reverseSplit	0.004	0.000	0.000
rowMedians	0.092	0.000	0.093
rowQ	0.016	0.000	0.018
selectChannels	0.028	0.000	0.030
selectSome	0.000	0.000	0.001
strbreak	0.016	0.000	0.017
subListExtract	0.684	0.008	0.690
testBioCConnection	0.008	0.004	0.412
updateOldESet	0.000	0.000	0.001
validMsg	0.000	0.000	0.001