BioC 3.6: CHECK report for Biobase on malbec1

Package: Biobase

Version: 2.37.2

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.37.2.tar.gz

StartedAt: 2017-08-15 21:31:41 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:32:59 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 77.9 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.37.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘2.37.2’
* 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-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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	0.004	0.030
ScalarObject-class	0.012	0.000	0.009
addVig2Menu	0.000	0.000	0.001
anyMissing	0.004	0.000	0.001
cache	0.004	0.000	0.003
channel	0.284	0.000	0.282
channelNames	0.120	0.000	0.119
class.AnnotatedDataFrame	0.032	0.000	0.033
class.ExpressionSet	0.388	0.008	0.396
class.MIAxE	0.024	0.000	0.023
class.MultiSet	0.036	0.000	0.035
class.NChannelSet	0.224	0.000	0.223
class.Versioned	0.068	0.000	0.069
class.VersionedBiobase	0.032	0.000	0.029
class.Versions	0.012	0.000	0.014
class.VersionsNull	0.000	0.000	0.002
class.container	0.004	0.000	0.004
class.eSet	0.096	0.000	0.093
classVersion	0.008	0.000	0.005
contents	0.000	0.000	0.001
copyEnv	0.028	0.000	0.028
copySubstitute	0.108	0.004	0.114
createPackage	0.004	0.000	0.007
data.aaMap	0.000	0.000	0.002
data.geneData	0.036	0.000	0.037
data.reporter	0.004	0.000	0.002
data.sample.ExpressionSet	0.02	0.00	0.02
data.sample.MultiSet	0.004	0.000	0.006
dumpPackTxt	0.000	0.000	0.016
esApply	1.488	0.008	1.497
getPkgVigs	0.008	0.000	0.015
isCurrent	0.032	0.000	0.035
isUnique	0.000	0.000	0.001
isVersioned	0.016	0.000	0.014
lcSuffix	0.036	0.000	0.036
listLen	0.004	0.000	0.001
makeDataPackage	0.112	0.000	0.114
matchpt	0.032	0.000	0.032
multiassign	0.000	0.000	0.002
note	0.000	0.000	0.001
openPDF	0.000	0.000	0.001
openVignette	0.004	0.000	0.000
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.016	0.000	0.016
read.MIAME	0.04	0.00	0.04
readExpressionSet	0.100	0.000	0.098
reverseSplit	0.004	0.000	0.001
rowMedians	0.128	0.004	0.131
rowQ	0.016	0.000	0.017
selectChannels	0.028	0.000	0.031
selectSome	0.000	0.000	0.001
strbreak	0.024	0.000	0.028
subListExtract	0.644	0.012	0.656
testBioCConnection	0.012	0.000	0.424
updateOldESet	0.000	0.000	0.001
validMsg	0.000	0.000	0.001