BioC 3.5: CHECK report for Biobase on toluca2

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: 2017-04-23 00:55:38 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 00:57:09 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 91.4 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 r72187)
* 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	0.043	0.003	0.046
ScalarObject-class	0.012	0.000	0.012
addVig2Menu	0.000	0.000	0.001
anyMissing	0.001	0.000	0.002
cache	0.003	0.000	0.004
channel	0.401	0.001	0.403
channelNames	0.081	0.001	0.081
class.AnnotatedDataFrame	0.039	0.001	0.040
class.ExpressionSet	0.378	0.014	0.392
class.MIAxE	0.016	0.001	0.017
class.MultiSet	0.034	0.000	0.034
class.NChannelSet	0.247	0.005	0.251
class.Versioned	0.061	0.003	0.063
class.VersionedBiobase	0.028	0.001	0.029
class.Versions	0.013	0.000	0.014
class.VersionsNull	0.001	0.000	0.001
class.container	0.005	0.000	0.005
class.eSet	0.083	0.001	0.084
classVersion	0.003	0.000	0.004
contents	0.001	0.001	0.001
copyEnv	0.027	0.000	0.026
copySubstitute	0.106	0.004	0.111
createPackage	0.005	0.001	0.006
data.aaMap	0.002	0.001	0.002
data.geneData	0.049	0.003	0.051
data.reporter	0.002	0.000	0.003
data.sample.ExpressionSet	0.013	0.008	0.020
data.sample.MultiSet	0.005	0.008	0.013
dumpPackTxt	0.004	0.001	0.005
esApply	1.443	0.017	1.461
getPkgVigs	0.009	0.001	0.010
isCurrent	0.030	0.000	0.031
isUnique	0.001	0.001	0.000
isVersioned	0.015	0.000	0.015
lcSuffix	0.03	0.00	0.03
listLen	0.001	0.000	0.001
makeDataPackage	0.094	0.009	0.103
matchpt	0.023	0.000	0.023
multiassign	0.001	0.000	0.001
note	0.001	0.000	0.000
openPDF	0	0	0
openVignette	0.001	0.000	0.001
package.version	0.001	0.000	0.002
read.AnnotatedDataFrame	0.013	0.001	0.014
read.MIAME	0.042	0.000	0.042
readExpressionSet	0.104	0.001	0.105
reverseSplit	0.001	0.000	0.001
rowMedians	0.041	0.002	0.043
rowQ	0.018	0.012	0.030
selectChannels	0.035	0.000	0.035
selectSome	0.000	0.001	0.001
strbreak	0.033	0.000	0.034
subListExtract	0.806	0.024	0.830
testBioCConnection	0.002	0.001	0.058
updateOldESet	0.000	0.000	0.001
validMsg	0.001	0.000	0.000