BioC 3.2: CHECK report for Biobase on linux1.bioconductor.org

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: 2015-10-27 01:22:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 01:23:57 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 83.5 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 3.2.2 (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 ‘2.30.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [21s/21s]
  Running ‘test-rowMedians.R’ [22s/22s]
 [44s/44s] 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	0.009	0.000	0.009
ScalarObject-class	0.015	0.000	0.015
addVig2Menu	0.000	0.000	0.001
anyMissing	0.002	0.000	0.002
cache	0.004	0.000	0.004
channel	0.146	0.000	0.146
channelNames	0.058	0.000	0.057
class.AnnotatedDataFrame	0.024	0.000	0.024
class.ExpressionSet	0.182	0.000	0.183
class.MIAxE	0.017	0.000	0.016
class.MultiSet	0.028	0.000	0.027
class.NChannelSet	0.184	0.000	0.185
class.Versioned	0.045	0.000	0.045
class.VersionedBiobase	0.021	0.000	0.020
class.Versions	0.012	0.000	0.011
class.VersionsNull	0.001	0.000	0.001
class.container	0.003	0.000	0.002
class.eSet	0.071	0.000	0.070
classVersion	0.004	0.000	0.004
contents	0.001	0.000	0.001
copyEnv	0.001	0.000	0.001
copySubstitute	0.008	0.000	0.008
createPackage	0.000	0.003	0.005
data.aaMap	0.002	0.000	0.001
data.geneData	0.024	0.000	0.023
data.reporter	0.001	0.000	0.001
data.sample.ExpressionSet	0.011	0.000	0.011
data.sample.MultiSet	0.000	0.003	0.005
dumpPackTxt	0.002	0.000	0.002
esApply	1.335	0.004	1.339
getPkgVigs	0.012	0.001	0.018
isCurrent	0.045	0.000	0.045
isUnique	0.001	0.000	0.001
isVersioned	0.018	0.000	0.018
lcSuffix	0.001	0.003	0.003
listLen	0.001	0.000	0.002
makeDataPackage	0.087	0.001	0.087
matchpt	0.006	0.000	0.006
multiassign	0.001	0.000	0.001
note	0	0	0
openPDF	0.001	0.000	0.001
openVignette	0.001	0.000	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.016	0.000	0.016
read.MIAME	0.003	0.000	0.003
readExpressionSet	0.076	0.000	0.076
reverseSplit	0.001	0.000	0.001
rowMedians	0.058	0.004	0.062
rowQ	0.021	0.003	0.025
selectChannels	0.064	0.001	0.064
selectSome	0.001	0.000	0.001
strbreak	0.002	0.000	0.002
subListExtract	1.288	0.004	1.292
testBioCConnection	0.013	0.000	0.034
updateOldESet	0.001	0.000	0.000
validMsg	0.001	0.000	0.001