BioC 3.6: CHECK report for Biobase on veracruz1

Package: Biobase

Version: 2.37.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.37.2.tar.gz

StartedAt: 2017-08-16 00:23:15 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:24:40 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 84.5 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_2.37.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Biobase.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 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   -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c envir.c -o envir.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matchpt.c -o matchpt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rowMedians.c -o rowMedians.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -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-3.6-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	0.037	0.002	0.041
ScalarObject-class	0.012	0.001	0.013
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.002
cache	0.006	0.000	0.006
channel	0.338	0.001	0.346
channelNames	0.076	0.000	0.077
class.AnnotatedDataFrame	0.047	0.000	0.048
class.ExpressionSet	0.379	0.006	0.402
class.MIAxE	0.019	0.000	0.020
class.MultiSet	0.031	0.001	0.031
class.NChannelSet	0.244	0.006	0.262
class.Versioned	0.055	0.001	0.056
class.VersionedBiobase	0.024	0.001	0.028
class.Versions	0.012	0.000	0.012
class.VersionsNull	0.001	0.000	0.002
class.container	0.003	0.000	0.003
class.eSet	0.070	0.001	0.080
classVersion	0.006	0.001	0.006
contents	0.001	0.000	0.001
copyEnv	0.017	0.000	0.017
copySubstitute	0.106	0.005	0.117
createPackage	0.005	0.002	0.008
data.aaMap	0.003	0.001	0.003
data.geneData	0.038	0.003	0.045
data.reporter	0.002	0.001	0.003
data.sample.ExpressionSet	0.012	0.003	0.015
data.sample.MultiSet	0.005	0.004	0.011
dumpPackTxt	0.003	0.001	0.005
esApply	1.339	0.007	1.383
getPkgVigs	0.007	0.001	0.007
isCurrent	0.031	0.000	0.032
isUnique	0.000	0.001	0.001
isVersioned	0.012	0.000	0.013
lcSuffix	0.032	0.001	0.037
listLen	0.001	0.000	0.002
makeDataPackage	0.083	0.005	0.089
matchpt	0.024	0.001	0.025
multiassign	0.001	0.000	0.002
note	0.000	0.000	0.001
openPDF	0.001	0.000	0.001
openVignette	0	0	0
package.version	0.002	0.000	0.001
read.AnnotatedDataFrame	0.016	0.001	0.017
read.MIAME	0.032	0.000	0.033
readExpressionSet	0.074	0.001	0.079
reverseSplit	0.001	0.000	0.001
rowMedians	0.038	0.003	0.042
rowQ	0.015	0.007	0.022
selectChannels	0.041	0.000	0.044
selectSome	0.000	0.000	0.001
strbreak	0.023	0.000	0.026
subListExtract	0.816	0.020	0.864
testBioCConnection	0.002	0.002	0.280
updateOldESet	0.001	0.000	0.001
validMsg	0.001	0.000	0.001