Package: Biobase

Version: 2.16.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.16.0.tar.gz

StartedAt: 2012-09-23 23:34:34 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:36:07 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 92.9 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Biobase.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘2.16.0’
* 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 whether package ‘Biobase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
.esApply: warning in multiassign(names(pData(X)), pData(X), env = e1):
  partial argument match of 'env' to 'envir'
Aggregate: warning in exists(nm, env = aggenv(agg), inherits = FALSE):
  partial argument match of 'env' to 'envir'
Aggregate: warning in assign(nm, env = aggenv(agg), initfun(agg)(nm,
  x)): partial argument match of 'env' to 'envir'
Aggregate: warning in get(nm, env = aggenv(agg)): partial argument
  match of 'env' to 'envir'
Aggregate: warning in assign(nm, aggfun(agg)(nm, v1), env =
  aggenv(agg)): partial argument match of 'env' to 'envir'
Aggregate: warning in assign(nm, env = aggenv(agg), initfun(agg)(nm,
  x[[i]])): partial argument match of 'env' to 'envir'
Aggregate: warning in assign(nm, env = aggenv(agg), aggfun(agg)(nm, v1,
  x[[i]])): partial argument match of 'env' to 'envir'
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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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-2.10-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-2.10-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-2.10-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-2.10-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-2.10-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/lib64 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘BiobaseDevelopment.Rnw’ 
   ‘Bioconductor.Rnw’ 
   ‘ExpressionSetIntroduction.Rnw’ 
   ‘HowTo.Rnw’ 
   ‘Qviews.Rnw’ 
   ‘esApply.Rnw’ 
** testing if installed package can be loaded

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.008	0.000	0.009
ScalarObject-class	0.012	0.000	0.016
addVig2Menu	0	0	0
anyMissing	0.004	0.000	0.001
biocReposList	0.060	0.004	0.108
cache	0.004	0.000	0.006
channel	0.280	0.020	0.537
channelNames	0.080	0.008	0.153
class.AnnotatedDataFrame	0.072	0.012	0.148
class.ExpressionSet	0.492	0.036	0.841
class.MIAxE	0.036	0.004	0.064
class.MultiSet	0.052	0.008	0.088
class.NChannelSet	0.320	0.000	0.347
class.Versioned	0.100	0.000	0.128
class.VersionedBiobase	0.048	0.004	0.068
class.Versions	0.020	0.000	0.024
class.VersionsNull	0.000	0.000	0.001
class.container	0.004	0.000	0.005
class.eSet	0.168	0.000	0.174
classVersion	0.012	0.000	0.013
contents	0	0	0
copyEnv	0.000	0.000	0.001
copySubstitute	0.012	0.000	0.012
createPackage	0.000	0.004	0.008
data.aaMap	0.000	0.000	0.002
data.geneData	0.028	0.008	0.036
data.reporter	0.004	0.000	0.002
data.sample.ExpressionSet	0.012	0.000	0.013
data.sample.MultiSet	0.004	0.000	0.005
dumpPackTxt	0.000	0.004	0.036
esApply	2.012	0.004	2.045
getPkgVigs	0.028	0.012	0.044
isCurrent	0.060	0.004	0.064
isUnique	0	0	0
isVersioned	0.024	0.004	0.028
lcSuffix	0.004	0.000	0.002
listLen	0.000	0.000	0.001
makeDataPackage	0.084	0.004	0.091
matchpt	0.008	0.000	0.009
multiassign	0.000	0.000	0.002
note	0.000	0.000	0.001
openPDF	0	0	0
openVignette	0.000	0.000	0.001
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.016	0.004	0.021
read.MIAME	0.004	0.000	0.007
readExpressionSet	0.096	0.000	0.097
reverseSplit	0	0	0
rowMedians	0.220	0.004	0.227
rowQ	0.020	0.004	0.022
selectChannels	0.112	0.000	0.112
selectSome	0	0	0
strbreak	0.004	0.000	0.003
subListExtract	3.916	0.068	3.988
testBioCConnection	0.004	0.000	0.010
updateOldESet	0	0	0
validMsg	0	0	0