BioC 2.13: CHECK report for Biobase on zin1

Package: Biobase

Version: 2.22.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.22.0.tar.gz

StartedAt: 2014-04-04 23:49:25 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:51:04 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 99.0 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Biobase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [5s/6s] 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘BiobaseDevelopment.Rnw’, ‘Bioconductor.Rnw’,
  ‘ExpressionSetIntroduction.Rnw’, ‘HowTo.Rnw’, ‘Qviews.Rnw’,
  ‘esApply.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [10s/11s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
subListExtract 5.436  0.064   5.603
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [23s/23s]
  Running ‘test-rowMedians.R’ [23s/23s]
 [46s/46s] 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/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	0.012	0.004	0.014
ScalarObject-class	0.016	0.000	0.019
addVig2Menu	0.004	0.000	0.003
anyMissing	0.000	0.004	0.003
cache	0.008	0.000	0.008
channel	0.144	0.000	0.148
channelNames	0.084	0.000	0.084
class.AnnotatedDataFrame	0.052	0.000	0.051
class.ExpressionSet	0.300	0.004	0.313
class.MIAxE	0.024	0.000	0.025
class.MultiSet	0.040	0.000	0.039
class.NChannelSet	0.220	0.000	0.221
class.Versioned	0.088	0.004	0.093
class.VersionedBiobase	0.096	0.000	0.099
class.Versions	0.016	0.000	0.019
class.VersionsNull	0.004	0.000	0.004
class.container	0.004	0.000	0.006
class.eSet	0.120	0.000	0.122
classVersion	0.012	0.000	0.013
contents	0.004	0.000	0.003
copyEnv	0.004	0.000	0.004
copySubstitute	0.024	0.000	0.025
createPackage	0.056	0.008	0.061
data.aaMap	0.004	0.000	0.004
data.geneData	0.032	0.000	0.031
data.reporter	0.004	0.000	0.004
data.sample.ExpressionSet	0.016	0.000	0.016
data.sample.MultiSet	0.008	0.000	0.007
dumpPackTxt	0.004	0.000	0.010
esApply	1.664	0.000	1.696
getPkgVigs	0.080	0.012	0.108
isCurrent	0.044	0.000	0.045
isUnique	0.000	0.000	0.003
isVersioned	0.02	0.00	0.02
lcSuffix	0.008	0.000	0.008
listLen	0.004	0.000	0.003
makeDataPackage	0.064	0.004	0.069
matchpt	0.008	0.000	0.009
multiassign	0.052	0.000	0.052
note	0.004	0.000	0.002
openPDF	0.004	0.000	0.002
openVignette	0.000	0.000	0.003
package.version	0.000	0.000	0.003
read.AnnotatedDataFrame	0.016	0.000	0.016
read.MIAME	0.004	0.000	0.005
readExpressionSet	0.072	0.004	0.076
reverseSplit	0.004	0.000	0.005
rowMedians	0.060	0.000	0.063
rowQ	0.020	0.004	0.023
selectChannels	0.060	0.004	0.066
selectSome	0.004	0.000	0.004
strbreak	0.008	0.000	0.006
subListExtract	5.436	0.064	5.603
testBioCConnection	0.000	0.004	0.013
updateOldESet	0.000	0.000	0.002
validMsg	0.000	0.004	0.005