Package: Biobase

Version: 2.16.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.16.0.tar.gz

StartedAt: 2012-03-31 23:52:15 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:53:24 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 69.0 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Biobase.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* 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/hpages/test-puck5/bbs-2.10-bioc/meat/Biobase.Rcheck/00check.log'
for details.

* installing *source* package 'Biobase' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c envir.c -o envir.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -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/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/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	0.008
ScalarObject-class	0.016	0.000	0.013
addVig2Menu	0	0	0
anyMissing	0.000	0.000	0.001
biocReposList	0.052	0.000	0.062
cache	0.004	0.000	0.002
channel	0.140	0.000	0.138
channelNames	0.036	0.000	0.037
class.AnnotatedDataFrame	0.036	0.000	0.036
class.ExpressionSet	0.292	0.004	0.300
class.MIAxE	0.020	0.000	0.021
class.MultiSet	0.040	0.000	0.038
class.NChannelSet	0.204	0.000	0.206
class.Versioned	0.068	0.004	0.075
class.VersionedBiobase	0.032	0.000	0.034
class.Versions	0.016	0.000	0.014
class.VersionsNull	0	0	0
class.container	0.004	0.000	0.003
class.eSet	0.124	0.000	0.124
classVersion	0.012	0.000	0.009
contents	0	0	0
copyEnv	0	0	0
copySubstitute	0.008	0.004	0.028
createPackage	0.008	0.004	0.033
data.aaMap	0.004	0.000	0.012
data.geneData	0.028	0.000	0.044
data.reporter	0.000	0.000	0.005
data.sample.ExpressionSet	0.012	0.000	0.015
data.sample.MultiSet	0.008	0.000	0.009
dumpPackTxt	0.000	0.000	0.002
esApply	1.988	0.004	1.994
getPkgVigs	0.032	0.004	0.056
isCurrent	0.052	0.000	0.054
isUnique	0	0	0
isVersioned	0.020	0.000	0.022
lcSuffix	0.004	0.000	0.001
listLen	0	0	0
makeDataPackage	0.068	0.004	0.087
matchpt	0.008	0.000	0.005
multiassign	0.000	0.000	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0	0	0
package.version	0	0	0
read.AnnotatedDataFrame	0.016	0.000	0.026
read.MIAME	0.004	0.000	0.004
readExpressionSet	0.084	0.000	0.095
reverseSplit	0.000	0.000	0.001
rowMedians	0.108	0.004	0.113
rowQ	0.020	0.004	0.025
selectChannels	0.072	0.004	0.074
selectSome	0	0	0
strbreak	0.000	0.000	0.001
subListExtract	2.200	0.028	2.227
testBioCConnection	0.000	0.000	0.011
updateOldESet	0	0	0
validMsg	0	0	0