BioC 3.5: CHECK report for Biobase on oaxaca

Package: Biobase

Version: 2.35.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.35.1.tar.gz

StartedAt: 2017-03-03 23:36:47 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:38:17 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 89.8 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.35.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Biobase.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.35.1’
* 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c envir.c -o envir.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c matchpt.c -o matchpt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c rowMedians.c -o rowMedians.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c sublist_extract.c -o sublist_extract.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.045	0.003	0.049
ScalarObject-class	0.016	0.000	0.016
addVig2Menu	0.000	0.000	0.001
anyMissing	0.002	0.001	0.002
cache	0.004	0.001	0.004
channel	0.372	0.001	0.373
channelNames	0.104	0.000	0.105
class.AnnotatedDataFrame	0.063	0.001	0.063
class.ExpressionSet	0.406	0.006	0.413
class.MIAxE	0.014	0.000	0.015
class.MultiSet	0.040	0.001	0.040
class.NChannelSet	0.267	0.004	0.270
class.Versioned	0.070	0.003	0.073
class.VersionedBiobase	0.020	0.000	0.019
class.Versions	0.015	0.001	0.015
class.VersionsNull	0.002	0.000	0.001
class.container	0.006	0.000	0.006
class.eSet	0.084	0.000	0.085
classVersion	0.005	0.000	0.005
contents	0.001	0.000	0.001
copyEnv	0.027	0.000	0.026
copySubstitute	0.102	0.004	0.106
createPackage	0.006	0.002	0.008
data.aaMap	0.003	0.001	0.004
data.geneData	0.060	0.004	0.063
data.reporter	0.003	0.001	0.004
data.sample.ExpressionSet	0.016	0.004	0.019
data.sample.MultiSet	0.006	0.003	0.009
dumpPackTxt	0.004	0.001	0.021
esApply	1.270	0.008	1.278
getPkgVigs	0.009	0.001	0.057
isCurrent	0.036	0.001	0.037
isUnique	0.000	0.000	0.001
isVersioned	0.018	0.001	0.018
lcSuffix	0.038	0.000	0.038
listLen	0.001	0.001	0.001
makeDataPackage	0.111	0.006	0.117
matchpt	0.033	0.000	0.033
multiassign	0.002	0.001	0.002
note	0.001	0.000	0.000
openPDF	0.000	0.000	0.001
openVignette	0.001	0.000	0.000
package.version	0.001	0.001	0.001
read.AnnotatedDataFrame	0.013	0.001	0.014
read.MIAME	0.045	0.000	0.044
readExpressionSet	0.112	0.001	0.112
reverseSplit	0.001	0.001	0.001
rowMedians	0.050	0.002	0.051
rowQ	0.019	0.007	0.026
selectChannels	0.052	0.001	0.052
selectSome	0.000	0.000	0.001
strbreak	0.034	0.000	0.035
subListExtract	0.936	0.018	0.955
testBioCConnection	0.003	0.001	0.975
updateOldESet	0.000	0.000	0.001
validMsg	0.001	0.000	0.001