BioC 3.1: CHECK report for Biobase on morelia

Package: Biobase

Version: 2.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.28.0.tar.gz

StartedAt: 2015-10-08 23:32:30 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:34:01 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 91.0 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_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Biobase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.28.0’
* 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 ... [6s/7s] 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 ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [22s/22s]
  Running ‘test-rowMedians.R’ [17s/17s]
 [39s/39s] 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-3.1-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	0.006	0.000	0.006
ScalarObject-class	0.016	0.001	0.017
addVig2Menu	0.001	0.000	0.001
anyMissing	0.001	0.000	0.002
cache	0.003	0.001	0.004
channel	0.121	0.001	0.122
channelNames	0.05	0.00	0.05
class.AnnotatedDataFrame	0.038	0.001	0.039
class.ExpressionSet	0.248	0.007	0.254
class.MIAxE	0.017	0.000	0.018
class.MultiSet	0.053	0.000	0.054
class.NChannelSet	0.211	0.005	0.216
class.Versioned	0.071	0.001	0.073
class.VersionedBiobase	0.024	0.000	0.024
class.Versions	0.017	0.001	0.018
class.VersionsNull	0.001	0.000	0.001
class.container	0.002	0.000	0.002
class.eSet	0.121	0.001	0.123
classVersion	0.008	0.000	0.008
contents	0.001	0.001	0.002
copyEnv	0.001	0.000	0.001
copySubstitute	0.011	0.004	0.015
createPackage	0.008	0.002	0.010
data.aaMap	0.003	0.001	0.004
data.geneData	0.057	0.004	0.062
data.reporter	0.002	0.000	0.003
data.sample.ExpressionSet	0.015	0.005	0.020
data.sample.MultiSet	0.006	0.004	0.010
dumpPackTxt	0.004	0.000	0.018
esApply	1.465	0.074	1.539
getPkgVigs	0.007	0.001	0.036
isCurrent	0.042	0.000	0.042
isUnique	0	0	0
isVersioned	0.011	0.001	0.011
lcSuffix	0.003	0.000	0.003
listLen	0.001	0.000	0.001
makeDataPackage	0.061	0.010	0.071
matchpt	0.004	0.001	0.007
multiassign	0.001	0.000	0.002
note	0	0	0
openPDF	0.000	0.001	0.001
openVignette	0.000	0.000	0.001
package.version	0.001	0.000	0.002
read.AnnotatedDataFrame	0.015	0.004	0.018
read.MIAME	0.002	0.001	0.002
readExpressionSet	0.114	0.012	0.126
reverseSplit	0	0	0
rowMedians	0.031	0.001	0.032
rowQ	0.015	0.007	0.022
selectChannels	0.076	0.005	0.082
selectSome	0.000	0.000	0.001
strbreak	0.001	0.000	0.002
subListExtract	0.929	0.082	1.011
testBioCConnection	0.003	0.001	0.405
updateOldESet	0.001	0.000	0.000
validMsg	0.001	0.000	0.001