BioC 2.13: CHECK report for Biobase on perceval

Package: Biobase

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.22.0.tar.gz

StartedAt: 2014-04-04 23:43:43 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:46:28 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 165.6 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Biobase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.22.0’
* 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 ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’
A package should be listed in only one of these fields.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘BiobaseDevelopment.Rnw’, ‘Bioconductor.Rnw’, ‘esApply.Rnw’,
  ‘ExpressionSetIntroduction.Rnw’, ‘HowTo.Rnw’, ‘Qviews.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
subListExtract 11.415  0.272  11.817
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [35s/36s]
  Running ‘test-rowMedians.R’ [33s/34s]
 [69s/70s] 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 were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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-2.13-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	0.022	0.001	0.023
ScalarObject-class	0.025	0.000	0.026
addVig2Menu	0.004	0.001	0.004
anyMissing	0.006	0.000	0.006
cache	0.017	0.002	0.022
channel	0.190	0.002	0.194
channelNames	0.096	0.001	0.098
class.AnnotatedDataFrame	0.067	0.002	0.068
class.ExpressionSet	0.351	0.020	0.372
class.MIAxE	0.034	0.001	0.034
class.MultiSet	0.049	0.001	0.050
class.NChannelSet	0.294	0.003	0.304
class.Versioned	0.119	0.002	0.121
class.VersionedBiobase	0.164	0.002	0.165
class.Versions	0.031	0.001	0.031
class.VersionsNull	0.006	0.000	0.007
class.container	0.009	0.000	0.010
class.eSet	0.152	0.004	0.158
classVersion	0.016	0.000	0.017
contents	0.008	0.000	0.009
copyEnv	0.009	0.000	0.009
copySubstitute	0.036	0.005	0.048
createPackage	0.115	0.005	0.151
data.aaMap	0.007	0.001	0.008
data.geneData	0.052	0.005	0.058
data.reporter	0.010	0.001	0.012
data.sample.ExpressionSet	0.020	0.007	0.026
data.sample.MultiSet	0.011	0.008	0.018
dumpPackTxt	0.007	0.001	0.156
esApply	2.040	0.029	2.097
getPkgVigs	0.064	0.010	0.395
isCurrent	0.069	0.002	0.070
isUnique	0.005	0.001	0.006
isVersioned	0.041	0.001	0.042
lcSuffix	0.024	0.000	0.024
listLen	0.006	0.000	0.007
makeDataPackage	0.086	0.009	0.095
matchpt	0.014	0.001	0.015
multiassign	0.009	0.001	0.010
note	0.003	0.000	0.004
openPDF	0.003	0.001	0.004
openVignette	0.004	0.000	0.003
package.version	0.004	0.000	0.005
read.AnnotatedDataFrame	0.022	0.002	0.023
read.MIAME	0.009	0.000	0.009
readExpressionSet	0.105	0.003	0.110
reverseSplit	0.010	0.001	0.011
rowMedians	0.063	0.005	0.069
rowQ	0.028	0.014	0.042
selectChannels	0.083	0.002	0.087
selectSome	0.006	0.000	0.006
strbreak	0.007	0.000	0.008
subListExtract	11.415	0.272	11.817
testBioCConnection	0.004	0.004	0.024
updateOldESet	0.002	0.003	0.005
validMsg	0.003	0.006	0.008