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: 2017-10-18 00:57:14 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:58:43 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 88.3 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 3.4.2 (2017-09-28)
* 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	0.036	0.002	0.039
ScalarObject-class	0.009	0.000	0.009
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.001	0.002
cache	0.005	0.000	0.006
channel	0.336	0.002	0.360
channelNames	0.086	0.001	0.088
class.AnnotatedDataFrame	0.043	0.001	0.045
class.ExpressionSet	0.343	0.006	0.355
class.MIAxE	0.015	0.000	0.016
class.MultiSet	0.023	0.001	0.024
class.NChannelSet	0.220	0.002	0.231
class.Versioned	0.054	0.005	0.059
class.VersionedBiobase	0.022	0.001	0.023
class.Versions	0.012	0.000	0.012
class.VersionsNull	0.001	0.000	0.001
class.container	0.001	0.000	0.002
class.eSet	0.074	0.001	0.076
classVersion	0.003	0.000	0.004
contents	0.001	0.000	0.002
copyEnv	0.020	0.001	0.021
copySubstitute	0.097	0.004	0.103
createPackage	0.006	0.001	0.011
data.aaMap	0.003	0.000	0.004
data.geneData	0.043	0.003	0.050
data.reporter	0.002	0.001	0.003
data.sample.ExpressionSet	0.013	0.005	0.018
data.sample.MultiSet	0.005	0.004	0.009
dumpPackTxt	0.003	0.000	0.004
esApply	1.313	0.014	1.362
getPkgVigs	0.007	0.001	0.010
isCurrent	0.031	0.000	0.033
isUnique	0.001	0.000	0.000
isVersioned	0.008	0.000	0.009
lcSuffix	0.032	0.000	0.035
listLen	0.001	0.000	0.002
makeDataPackage	0.091	0.007	0.099
matchpt	0.021	0.000	0.021
multiassign	0.022	0.000	0.024
note	0.001	0.000	0.001
openPDF	0	0	0
openVignette	0.000	0.000	0.001
package.version	0.002	0.000	0.001
read.AnnotatedDataFrame	0.011	0.000	0.013
read.MIAME	0.03	0.00	0.03
readExpressionSet	0.078	0.001	0.080
reverseSplit	0.001	0.000	0.001
rowMedians	0.041	0.003	0.043
rowQ	0.016	0.007	0.023
selectChannels	0.037	0.000	0.038
selectSome	0.001	0.000	0.001
strbreak	0.028	0.001	0.029
subListExtract	0.754	0.022	0.801
testBioCConnection	0.002	0.001	0.266
updateOldESet	0.001	0.000	0.000
validMsg	0.001	0.000	0.000