Package: Biobase

Version: 2.18.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.18.0.tar.gz

StartedAt: 2013-03-24 23:36:05 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:38:21 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 135.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Biobase.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.18.0’
* 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 ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
See ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Biobase.Rcheck/00install.out’ for details.
* 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 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 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
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
Examples with CPU or elapsed time > 5s
                 user system elapsed
subListExtract 12.137  0.156  12.481
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’
  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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
In file included from Rinit.c:3:0:
/home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c envir.c -o envir.o
In file included from envir.c:5:0:
/home/biocbuild/bbs-2.11-bioc/R/include/R_ext/RConverters.h:32:2: warning: #warning "R_ext/RConverters.h was deprecated in R 2.15.1 and will be removed in R 3.0.0" [-Wcpp]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-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-2.11-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-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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	0.016	0.000	0.019
addVig2Menu	0.000	0.000	0.001
anyMissing	0.000	0.000	0.001
cache	0.004	0.000	0.004
channel	0.200	0.004	0.206
channelNames	0.056	0.000	0.056
class.AnnotatedDataFrame	0.056	0.000	0.056
class.ExpressionSet	0.476	0.004	0.506
class.MIAxE	0.020	0.008	0.027
class.MultiSet	0.052	0.000	0.055
class.NChannelSet	0.256	0.000	0.258
class.Versioned	0.100	0.000	0.099
class.VersionedBiobase	0.048	0.000	0.048
class.Versions	0.024	0.000	0.022
class.VersionsNull	0.000	0.000	0.001
class.container	0.004	0.000	0.004
class.eSet	0.188	0.004	0.192
classVersion	0.008	0.004	0.011
contents	0.004	0.000	0.000
copyEnv	0.000	0.000	0.001
copySubstitute	0.008	0.004	0.010
createPackage	0.008	0.000	0.009
data.aaMap	0.004	0.000	0.003
data.geneData	0.032	0.004	0.036
data.reporter	0.004	0.000	0.002
data.sample.ExpressionSet	0.008	0.004	0.013
data.sample.MultiSet	0.004	0.000	0.005
dumpPackTxt	0.004	0.000	0.017
esApply	2.236	0.004	2.240
getPkgVigs	0.032	0.012	0.117
isCurrent	0.064	0.000	0.136
isUnique	0	0	0
isVersioned	0.024	0.000	0.048
lcSuffix	0.000	0.000	0.002
listLen	0.004	0.000	0.001
makeDataPackage	0.072	0.000	0.123
matchpt	0.004	0.000	0.007
multiassign	0.004	0.000	0.001
note	0	0	0
openPDF	0	0	0
openVignette	0.000	0.000	0.001
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.024	0.000	0.056
read.MIAME	0.008	0.000	0.007
readExpressionSet	0.096	0.000	0.099
reverseSplit	0.004	0.000	0.000
rowMedians	0.068	0.000	0.067
rowQ	0.020	0.004	0.025
selectChannels	0.100	0.000	0.097
selectSome	0	0	0
strbreak	0.004	0.000	0.001
subListExtract	12.137	0.156	12.481
testBioCConnection	0.000	0.000	0.023
updateOldESet	0	0	0
validMsg	0	0	0