BioC 3.0: CHECK report for Biobase on perceval

Package: Biobase

Version: 2.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.26.0.tar.gz

StartedAt: 2015-04-09 23:05:39 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:07:58 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 139.3 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Biobase.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [9s/15s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [30s/30s]
  Running ‘test-rowMedians.R’ [28s/28s]
 [59s/59s] 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Rinit.c -o Rinit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c anyMissing.c -o anyMissing.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c envir.c -o envir.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matchpt.c -o matchpt.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c rowMedians.c -o rowMedians.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sublist_extract.c -o sublist_extract.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.009	0.000	0.008
ScalarObject-class	0.018	0.000	0.018
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.002
cache	0.004	0.001	0.010
channel	0.227	0.004	0.234
channelNames	0.075	0.001	0.076
class.AnnotatedDataFrame	0.039	0.001	0.040
class.ExpressionSet	0.308	0.011	0.319
class.MIAxE	0.024	0.000	0.024
class.MultiSet	0.042	0.000	0.043
class.NChannelSet	0.333	0.005	0.339
class.Versioned	0.093	0.002	0.095
class.VersionedBiobase	0.046	0.001	0.048
class.Versions	0.018	0.001	0.018
class.VersionsNull	0.002	0.001	0.002
class.container	0.004	0.000	0.005
class.eSet	0.123	0.002	0.125
classVersion	0.007	0.000	0.007
contents	0.002	0.001	0.002
copyEnv	0.001	0.000	0.002
copySubstitute	0.016	0.007	0.045
createPackage	0.010	0.004	0.014
data.aaMap	0.004	0.000	0.004
data.geneData	0.040	0.004	0.045
data.reporter	0.002	0.001	0.003
data.sample.ExpressionSet	0.015	0.006	0.021
data.sample.MultiSet	0.006	0.004	0.010
dumpPackTxt	0.002	0.001	0.023
esApply	1.742	0.010	1.754
getPkgVigs	0.050	0.007	0.101
isCurrent	0.045	0.000	0.046
isUnique	0.001	0.000	0.001
isVersioned	0.019	0.001	0.018
lcSuffix	0.004	0.000	0.004
listLen	0.001	0.000	0.002
makeDataPackage	0.078	0.008	0.086
matchpt	0.007	0.001	0.007
multiassign	0.002	0.000	0.002
note	0.001	0.001	0.001
openPDF	0.001	0.000	0.001
openVignette	0.000	0.000	0.001
package.version	0.001	0.000	0.002
read.AnnotatedDataFrame	0.014	0.001	0.017
read.MIAME	0.002	0.000	0.003
readExpressionSet	0.095	0.003	0.099
reverseSplit	0.001	0.000	0.002
rowMedians	0.180	0.005	0.185
rowQ	0.020	0.011	0.031
selectChannels	0.083	0.001	0.083
selectSome	0.001	0.000	0.001
strbreak	0.002	0.000	0.002
subListExtract	2.390	0.058	2.457
testBioCConnection	0.003	0.001	0.120
updateOldESet	0.000	0.000	0.001
validMsg	0.001	0.000	0.002