BioC 3.4: CHECK report for Biobase on zin1

Package: Biobase

Version: 2.33.3

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.33.3.tar.gz

StartedAt: 2016-09-20 03:41:32 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:42:38 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 66.7 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.33.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Biobase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.33.3’
* 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 sizes of PDF files under ‘inst/doc’ ... 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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	0.004	0.000	0.005
ScalarObject-class	0.012	0.000	0.009
addVig2Menu	0	0	0
anyMissing	0.004	0.000	0.002
cache	0.000	0.000	0.003
channel	0.084	0.000	0.086
channelNames	0.044	0.000	0.044
class.AnnotatedDataFrame	0.024	0.000	0.024
class.ExpressionSet	0.172	0.004	0.177
class.MIAxE	0.016	0.000	0.014
class.MultiSet	0.028	0.000	0.026
class.NChannelSet	0.132	0.004	0.136
class.Versioned	0.052	0.000	0.049
class.VersionedBiobase	0.020	0.000	0.021
class.Versions	0.012	0.000	0.012
class.VersionsNull	0.004	0.000	0.001
class.container	0.004	0.000	0.003
class.eSet	0.072	0.000	0.071
classVersion	0.004	0.000	0.004
contents	0.000	0.000	0.001
copyEnv	0	0	0
copySubstitute	0.008	0.000	0.009
createPackage	0.008	0.000	0.005
data.aaMap	0.000	0.000	0.002
data.geneData	0.028	0.000	0.026
data.reporter	0.004	0.000	0.002
data.sample.ExpressionSet	0.052	0.000	0.052
data.sample.MultiSet	0.000	0.004	0.005
dumpPackTxt	0.000	0.000	0.009
esApply	1.096	0.004	1.099
getPkgVigs	0.008	0.000	0.035
isCurrent	0.024	0.000	0.027
isUnique	0	0	0
isVersioned	0.008	0.000	0.010
lcSuffix	0.000	0.000	0.002
listLen	0.004	0.000	0.001
makeDataPackage	0.056	0.004	0.061
matchpt	0.008	0.000	0.005
multiassign	0.000	0.000	0.001
note	0.000	0.000	0.001
openPDF	0.004	0.000	0.001
openVignette	0	0	0
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.012	0.000	0.013
read.MIAME	0.000	0.000	0.002
readExpressionSet	0.048	0.000	0.048
reverseSplit	0.000	0.000	0.001
rowMedians	0.040	0.000	0.037
rowQ	0.016	0.000	0.017
selectChannels	0.036	0.004	0.039
selectSome	0	0	0
strbreak	0.000	0.000	0.001
subListExtract	0.704	0.008	0.712
testBioCConnection	0.032	0.004	0.608
updateOldESet	0	0	0
validMsg	0.000	0.000	0.001