BioC 3.0: CHECK report for Biobase on zin1

Package: Biobase

Version: 2.26.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.26.0.tar.gz

StartedAt: 2015-04-09 21:56:28 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 21:57:58 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 89.3 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/Biobase.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.26.0’
* 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/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘tkWidgets’ ‘tools’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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’
read.MIAME: no visible global function definition for ‘tkMIAME’
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [21s/21s]
  Running ‘test-rowMedians.R’ [22s/22s]
 [43s/44s] 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
* DONE

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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-3.0-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/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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	0.008	0.000	0.008
ScalarObject-class	0.012	0.000	0.014
addVig2Menu	0.004	0.000	0.001
anyMissing	0.000	0.000	0.001
cache	0.004	0.000	0.005
channel	0.164	0.000	0.163
channelNames	0.064	0.000	0.062
class.AnnotatedDataFrame	0.032	0.000	0.033
class.ExpressionSet	0.240	0.000	0.237
class.MIAxE	0.020	0.000	0.021
class.MultiSet	0.036	0.000	0.036
class.NChannelSet	0.248	0.000	0.251
class.Versioned	0.072	0.000	0.071
class.VersionedBiobase	0.028	0.000	0.031
class.Versions	0.016	0.000	0.016
class.VersionsNull	0.000	0.000	0.002
class.container	0.000	0.000	0.003
class.eSet	0.108	0.000	0.109
classVersion	0.008	0.000	0.006
contents	0.004	0.000	0.001
copyEnv	0.000	0.000	0.001
copySubstitute	0.012	0.000	0.011
createPackage	0.000	0.008	0.008
data.aaMap	0.004	0.000	0.003
data.geneData	0.032	0.000	0.031
data.reporter	0.000	0.000	0.002
data.sample.ExpressionSet	0.012	0.000	0.013
data.sample.MultiSet	0.008	0.000	0.005
dumpPackTxt	0.000	0.000	0.012
esApply	1.528	0.000	1.532
getPkgVigs	0.032	0.000	0.061
isCurrent	0.04	0.00	0.04
isUnique	0.000	0.000	0.001
isVersioned	0.016	0.000	0.016
lcSuffix	0.000	0.000	0.003
listLen	0.000	0.000	0.001
makeDataPackage	0.064	0.004	0.067
matchpt	0.004	0.004	0.006
multiassign	0.000	0.000	0.001
note	0.004	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	0.012	0.000	0.013
read.MIAME	0.000	0.000	0.002
readExpressionSet	0.064	0.004	0.070
reverseSplit	0.004	0.000	0.001
rowMedians	0.104	0.000	0.104
rowQ	0.02	0.00	0.02
selectChannels	0.056	0.000	0.055
selectSome	0.000	0.000	0.001
strbreak	0.000	0.000	0.001
subListExtract	1.324	0.012	1.337
testBioCConnection	0.004	0.000	0.015
updateOldESet	0.000	0.000	0.001
validMsg	0.000	0.000	0.001