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BioC 2.14: CHECK report for Biobase on morelia

This page was generated on 2014-10-08 09:01:57 -0700 (Wed, 08 Oct 2014).

Package 83/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.24.0
Bioconductor Package Maintainer
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Biobase
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: Biobase
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.24.0.tar.gz
StartedAt: 2014-10-07 21:26:53 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:28:43 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 109.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Biobase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.24.0’
* 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 ... [7s/7s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [26s/26s]
  Running ‘test-rowMedians.R’ [20s/20s]
 [45s/46s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/Biobase.Rcheck/00check.log’
for details.

Biobase.Rcheck/00install.out:

* installing *source* package ‘Biobase’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c envir.c -o envir.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matchpt.c -o matchpt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c rowMedians.c -o rowMedians.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sublist_extract.c -o sublist_extract.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.14-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)

Biobase.Rcheck/Biobase-Ex.timings:

nameusersystemelapsed
Aggregate0.0080.0000.009
ScalarObject-class0.0180.0010.018
addVig2Menu0.0010.0000.001
anyMissing0.0010.0000.001
cache0.0040.0020.005
channel0.1850.0020.186
channelNames0.0670.0000.068
class.AnnotatedDataFrame0.0440.0010.044
class.ExpressionSet0.3270.0080.335
class.MIAxE0.0250.0010.026
class.MultiSet0.0460.0010.046
class.NChannelSet0.3060.0030.309
class.Versioned0.0890.0010.090
class.VersionedBiobase0.0340.0000.034
class.Versions0.0160.0010.016
class.VersionsNull0.0010.0000.001
class.container0.0030.0000.004
class.eSet0.1170.0010.118
classVersion0.0070.0000.008
contents0.0010.0010.002
copyEnv0.0010.0000.001
copySubstitute0.0130.0040.017
createPackage0.0080.0020.011
data.aaMap0.0030.0000.003
data.geneData0.0460.0010.048
data.reporter0.0010.0000.002
data.sample.ExpressionSet0.0140.0040.018
data.sample.MultiSet0.0060.0050.011
dumpPackTxt0.0050.0010.026
esApply1.8210.0091.845
getPkgVigs0.0390.0060.077
isCurrent0.0510.0010.053
isUnique0.0010.0000.001
isVersioned0.0230.0000.024
lcSuffix0.0020.0000.002
listLen0.0010.0010.001
makeDataPackage0.0740.0080.082
matchpt0.0050.0000.006
multiassign0.0020.0000.001
note000
openPDF000
openVignette0.0010.0000.001
package.version0.0020.0010.002
read.AnnotatedDataFrame0.0170.0010.018
read.MIAME0.0020.0000.002
readExpressionSet0.1010.0020.103
reverseSplit0.0000.0000.001
rowMedians0.1000.0030.103
rowQ0.0210.0080.031
selectChannels0.0650.0010.067
selectSome000
strbreak0.0020.0000.002
subListExtract1.5110.0271.539
testBioCConnection0.0020.0010.012
updateOldESet0.0010.0000.000
validMsg0.0000.0000.001