BioC 2.14: CHECK report for Biobase on petty

Package: Biobase

Version: 2.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.24.0.tar.gz

StartedAt: 2014-10-07 20:54:16 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:57:28 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 191.2 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 --no-multiarch Biobase_2.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Biobase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.24.0’
* 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 ... [11s/12s] 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 ... NOTE
cache: no visible binding for global variable ‘cache_old’
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [12s/12s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [45s/45s]
  Running ‘test-rowMedians.R’ [36s/36s]
 [81s/82s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Rinit.c -o Rinit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c anyMissing.c -o anyMissing.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c envir.c -o envir.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matchpt.c -o matchpt.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c rowMedians.c -o rowMedians.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sublist_extract.c -o sublist_extract.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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-2.14-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	0.021	0.001	0.022
ScalarObject-class	0.031	0.000	0.032
addVig2Menu	0.001	0.000	0.002
anyMissing	0.003	0.000	0.004
cache	0.006	0.001	0.008
channel	0.351	0.004	0.356
channelNames	0.140	0.001	0.141
class.AnnotatedDataFrame	0.079	0.002	0.080
class.ExpressionSet	0.555	0.019	0.574
class.MIAxE	0.043	0.001	0.044
class.MultiSet	0.079	0.000	0.080
class.NChannelSet	0.553	0.006	0.560
class.Versioned	0.141	0.001	0.143
class.VersionedBiobase	0.063	0.002	0.064
class.Versions	0.031	0.001	0.031
class.VersionsNull	0.003	0.000	0.003
class.container	0.011	0.000	0.010
class.eSet	0.223	0.002	0.225
classVersion	0.013	0.001	0.012
contents	0.002	0.000	0.003
copyEnv	0.002	0.000	0.002
copySubstitute	0.021	0.008	0.034
createPackage	0.014	0.005	0.018
data.aaMap	0.005	0.001	0.006
data.geneData	0.062	0.005	0.068
data.reporter	0.009	0.001	0.009
data.sample.ExpressionSet	0.024	0.013	0.038
data.sample.MultiSet	0.009	0.011	0.021
dumpPackTxt	0.003	0.001	0.026
esApply	3.169	0.019	3.191
getPkgVigs	0.082	0.012	0.145
isCurrent	0.088	0.001	0.089
isUnique	0.002	0.001	0.002
isVersioned	0.035	0.000	0.035
lcSuffix	0.006	0.000	0.005
listLen	0.002	0.001	0.003
makeDataPackage	0.118	0.016	0.140
matchpt	0.009	0.001	0.010
multiassign	0.002	0.000	0.002
note	0.001	0.001	0.002
openPDF	0.001	0.000	0.000
openVignette	0.001	0.000	0.001
package.version	0.005	0.000	0.006
read.AnnotatedDataFrame	0.024	0.003	0.026
read.MIAME	0.006	0.000	0.005
readExpressionSet	0.144	0.004	0.147
reverseSplit	0.001	0.001	0.002
rowMedians	0.170	0.003	0.172
rowQ	0.030	0.016	0.052
selectChannels	0.132	0.000	0.133
selectSome	0.001	0.000	0.002
strbreak	0.003	0.000	0.003
subListExtract	2.712	0.056	2.771
testBioCConnection	0.004	0.002	0.016
updateOldESet	0.001	0.000	0.001
validMsg	0.001	0.001	0.001