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BioC 3.2: CHECK report for Biobase on oaxaca

This page was generated on 2016-04-23 10:22:35 -0700 (Sat, 23 Apr 2016).

Package 93/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.30.0
Bioconductor Package Maintainer
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Biobase
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Biobase
Version: 2.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.30.0.tar.gz
StartedAt: 2016-04-22 22:06:18 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:07:54 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 96.9 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 Biobase_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Biobase.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.30.0’
* 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 ... [6s/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 ... OK
* 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 ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [22s/22s]
  Running ‘test-rowMedians.R’ [18s/18s]
 [40s/40s] 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

Status: OK

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/Library/Frameworks/R.framework/Resources/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-3.2-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
Aggregate0.0090.0000.009
ScalarObject-class0.0140.0000.015
addVig2Menu0.0010.0000.001
anyMissing0.0010.0000.001
cache0.0040.0010.005
channel0.1620.0010.163
channelNames0.0830.0000.084
class.AnnotatedDataFrame0.0430.0010.044
class.ExpressionSet0.3010.0060.308
class.MIAxE0.0280.0000.029
class.MultiSet0.0500.0010.050
class.NChannelSet0.2620.0050.268
class.Versioned0.0790.0000.081
class.VersionedBiobase0.0290.0000.030
class.Versions0.0180.0010.018
class.VersionsNull0.0010.0000.001
class.container0.0040.0000.004
class.eSet0.1150.0000.116
classVersion0.0070.0000.006
contents0.0010.0010.002
copyEnv0.0010.0000.001
copySubstitute0.0130.0040.019
createPackage0.0050.0010.007
data.aaMap0.0030.0000.003
data.geneData0.0580.0040.061
data.reporter0.0030.0010.003
data.sample.ExpressionSet0.0150.0020.018
data.sample.MultiSet0.0060.0020.008
dumpPackTxt0.0040.0010.023
esApply1.6600.0091.670
getPkgVigs0.0130.0020.087
isCurrent0.0510.0010.052
isUnique000
isVersioned0.0170.0010.017
lcSuffix0.0030.0000.004
listLen0.0020.0000.002
makeDataPackage0.0740.0040.137
matchpt0.0050.0010.006
multiassign0.0010.0000.002
note0.0000.0000.001
openPDF0.0000.0010.001
openVignette0.0010.0000.001
package.version0.0010.0000.002
read.AnnotatedDataFrame0.0150.0010.016
read.MIAME0.0030.0000.004
readExpressionSet0.1250.0010.125
reverseSplit0.0010.0000.001
rowMedians0.0440.0010.045
rowQ0.0180.0050.024
selectChannels0.0560.0000.056
selectSome0.0010.0000.001
strbreak0.0020.0000.002
subListExtract0.9720.0210.994
testBioCConnection0.0030.0010.663
updateOldESet000
validMsg0.0010.0000.001