BioC 3.4: CHECK report for Biobase on morelia

Package: Biobase

Version: 2.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.34.0.tar.gz

StartedAt: 2017-04-14 23:08:28 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:09:56 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 87.8 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_2.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Biobase.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.34.0’
* 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 ... 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-3.4-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	0.009	0.001	0.009
ScalarObject-class	0.012	0.000	0.012
addVig2Menu	0.001	0.000	0.001
anyMissing	0.001	0.000	0.001
cache	0.003	0.000	0.004
channel	0.088	0.000	0.089
channelNames	0.045	0.000	0.045
class.AnnotatedDataFrame	0.028	0.000	0.029
class.ExpressionSet	0.266	0.007	0.273
class.MIAxE	0.018	0.000	0.019
class.MultiSet	0.038	0.000	0.039
class.NChannelSet	0.208	0.002	0.209
class.Versioned	0.054	0.001	0.055
class.VersionedBiobase	0.032	0.001	0.032
class.Versions	0.018	0.000	0.018
class.VersionsNull	0.002	0.001	0.002
class.container	0.005	0.000	0.006
class.eSet	0.158	0.001	0.160
classVersion	0.004	0.000	0.004
contents	0.001	0.000	0.002
copyEnv	0.001	0.001	0.001
copySubstitute	0.008	0.003	0.011
createPackage	0.005	0.001	0.007
data.aaMap	0.002	0.001	0.002
data.geneData	0.052	0.004	0.056
data.reporter	0.003	0.001	0.003
data.sample.ExpressionSet	0.011	0.003	0.013
data.sample.MultiSet	0.005	0.003	0.007
dumpPackTxt	0.003	0.001	0.023
esApply	1.349	0.008	1.358
getPkgVigs	0.010	0.001	0.090
isCurrent	0.033	0.001	0.034
isUnique	0.001	0.000	0.001
isVersioned	0.01	0.00	0.01
lcSuffix	0.003	0.000	0.004
listLen	0.001	0.000	0.001
makeDataPackage	0.064	0.005	0.068
matchpt	0.007	0.001	0.007
multiassign	0.002	0.000	0.002
note	0.001	0.000	0.000
openPDF	0.001	0.001	0.000
openVignette	0.001	0.000	0.001
package.version	0.001	0.000	0.002
read.AnnotatedDataFrame	0.015	0.001	0.017
read.MIAME	0.003	0.000	0.003
readExpressionSet	0.091	0.001	0.092
reverseSplit	0.000	0.000	0.001
rowMedians	0.080	0.002	0.081
rowQ	0.013	0.005	0.018
selectChannels	0.042	0.002	0.044
selectSome	0.001	0.000	0.001
strbreak	0.001	0.000	0.002
subListExtract	0.782	0.021	0.804
testBioCConnection	0.002	0.001	0.965
updateOldESet	0	0	0
validMsg	0.001	0.000	0.001