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BioC 3.4: CHECK report for Biobase on zin1

This page was generated on 2016-09-21 03:35:35 -0700 (Wed, 21 Sep 2016).

Package 104/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.33.3
Bioconductor Package Maintainer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase
Last Changed Rev: 120598 / Revision: 121152
Last Changed Date: 2016-08-30 15:21:43 -0700 (Tue, 30 Aug 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biobase
Version: 2.33.3
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.33.3.tar.gz
StartedAt: 2016-09-20 03:41:32 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:42:38 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 66.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.33.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Biobase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.33.3’
* 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 ... 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 ... OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Biobase.Rcheck/00install.out:

* installing *source* package ‘Biobase’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sublist_extract.c -o sublist_extract.o
gcc -shared -L/home/biocbuild/bbs-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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
Aggregate0.0040.0000.005
ScalarObject-class0.0120.0000.009
addVig2Menu000
anyMissing0.0040.0000.002
cache0.0000.0000.003
channel0.0840.0000.086
channelNames0.0440.0000.044
class.AnnotatedDataFrame0.0240.0000.024
class.ExpressionSet0.1720.0040.177
class.MIAxE0.0160.0000.014
class.MultiSet0.0280.0000.026
class.NChannelSet0.1320.0040.136
class.Versioned0.0520.0000.049
class.VersionedBiobase0.0200.0000.021
class.Versions0.0120.0000.012
class.VersionsNull0.0040.0000.001
class.container0.0040.0000.003
class.eSet0.0720.0000.071
classVersion0.0040.0000.004
contents0.0000.0000.001
copyEnv000
copySubstitute0.0080.0000.009
createPackage0.0080.0000.005
data.aaMap0.0000.0000.002
data.geneData0.0280.0000.026
data.reporter0.0040.0000.002
data.sample.ExpressionSet0.0520.0000.052
data.sample.MultiSet0.0000.0040.005
dumpPackTxt0.0000.0000.009
esApply1.0960.0041.099
getPkgVigs0.0080.0000.035
isCurrent0.0240.0000.027
isUnique000
isVersioned0.0080.0000.010
lcSuffix0.0000.0000.002
listLen0.0040.0000.001
makeDataPackage0.0560.0040.061
matchpt0.0080.0000.005
multiassign0.0000.0000.001
note0.0000.0000.001
openPDF0.0040.0000.001
openVignette000
package.version0.0000.0000.001
read.AnnotatedDataFrame0.0120.0000.013
read.MIAME0.0000.0000.002
readExpressionSet0.0480.0000.048
reverseSplit0.0000.0000.001
rowMedians0.0400.0000.037
rowQ0.0160.0000.017
selectChannels0.0360.0040.039
selectSome000
strbreak0.0000.0000.001
subListExtract0.7040.0080.712
testBioCConnection0.0320.0040.608
updateOldESet000
validMsg0.0000.0000.001