BioC 3.5: CHECK report for Biobase on veracruz2

Package: Biobase

Version: 2.36.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.36.2.tar.gz

StartedAt: 2017-08-16 00:12:11 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:13:39 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 88.0 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_2.36.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘2.36.2’
* 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-3.5-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	0.015	0.000	0.015
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.002
cache	0.007	0.000	0.007
channel	0.403	0.001	0.422
channelNames	0.093	0.000	0.097
class.AnnotatedDataFrame	0.041	0.000	0.042
class.ExpressionSet	0.382	0.005	0.406
class.MIAxE	0.019	0.001	0.022
class.MultiSet	0.03	0.00	0.03
class.NChannelSet	0.250	0.006	0.269
class.Versioned	0.061	0.001	0.063
class.VersionedBiobase	0.024	0.001	0.025
class.Versions	0.012	0.000	0.013
class.VersionsNull	0.001	0.000	0.002
class.container	0.003	0.000	0.004
class.eSet	0.082	0.001	0.086
classVersion	0.005	0.000	0.008
contents	0.001	0.001	0.002
copyEnv	0.022	0.000	0.023
copySubstitute	0.108	0.004	0.118
createPackage	0.006	0.001	0.009
data.aaMap	0.002	0.001	0.003
data.geneData	0.042	0.003	0.046
data.reporter	0.002	0.001	0.003
data.sample.ExpressionSet	0.013	0.003	0.019
data.sample.MultiSet	0.005	0.003	0.008
dumpPackTxt	0.003	0.001	0.004
esApply	1.423	0.010	1.489
getPkgVigs	0.010	0.001	0.013
isCurrent	0.032	0.000	0.032
isUnique	0.001	0.001	0.001
isVersioned	0.012	0.000	0.012
lcSuffix	0.034	0.001	0.035
listLen	0.002	0.000	0.001
makeDataPackage	0.084	0.006	0.092
matchpt	0.026	0.000	0.028
multiassign	0.002	0.000	0.002
note	0.001	0.000	0.001
openPDF	0.000	0.000	0.001
openVignette	0.001	0.000	0.001
package.version	0.002	0.001	0.002
read.AnnotatedDataFrame	0.015	0.001	0.017
read.MIAME	0.032	0.000	0.035
readExpressionSet	0.093	0.002	0.098
reverseSplit	0.001	0.000	0.001
rowMedians	0.043	0.003	0.046
rowQ	0.017	0.007	0.024
selectChannels	0.042	0.000	0.045
selectSome	0.001	0.000	0.001
strbreak	0.027	0.000	0.027
subListExtract	0.838	0.020	0.894
testBioCConnection	0.003	0.002	0.287
updateOldESet	0.001	0.000	0.001
validMsg	0.001	0.000	0.001