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BioC 3.4: CHECK report for Biobase on malbec1

This page was generated on 2017-04-15 16:08:41 -0400 (Sat, 15 Apr 2017).

Package 108/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.34.0
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Biobase
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: 2.34.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.34.0.tar.gz
StartedAt: 2017-04-14 21:13:00 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:14:16 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 76.2 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_2.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Biobase.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.34.0’
* 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 ... 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 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
Aggregate0.0040.0000.006
ScalarObject-class0.0120.0000.010
addVig2Menu0.0000.0000.001
anyMissing0.0040.0000.002
cache0.0040.0000.004
channel0.1040.0000.102
channelNames0.0480.0000.047
class.AnnotatedDataFrame0.0280.0000.029
class.ExpressionSet0.1920.0080.202
class.MIAxE0.0120.0000.015
class.MultiSet0.0280.0000.028
class.NChannelSet0.1880.0000.188
class.Versioned0.0440.0000.045
class.VersionedBiobase0.020.000.02
class.Versions0.0080.0000.010
class.VersionsNull0.0000.0040.001
class.container0.0040.0000.004
class.eSet0.0640.0040.068
classVersion0.0040.0000.004
contents0.0000.0040.001
copyEnv0.0000.0000.001
copySubstitute0.0080.0000.009
createPackage0.0040.0000.005
data.aaMap0.0000.0000.001
data.geneData0.0160.0040.023
data.reporter0.0000.0000.002
data.sample.ExpressionSet0.0080.0000.012
data.sample.MultiSet0.0040.0000.005
dumpPackTxt0.0040.0000.013
esApply1.1640.0001.164
getPkgVigs0.0080.0000.021
isCurrent0.0240.0000.024
isUnique000
isVersioned0.0160.0000.013
lcSuffix0.0040.0000.003
listLen0.0000.0000.001
makeDataPackage0.0840.0000.084
matchpt0.0040.0000.005
multiassign0.0000.0000.001
note0.0040.0000.000
openPDF0.0000.0000.001
openVignette0.0040.0000.001
package.version0.0000.0000.001
read.AnnotatedDataFrame0.0160.0000.015
read.MIAME0.0040.0000.003
readExpressionSet0.0720.0000.072
reverseSplit0.0000.0000.001
rowMedians0.1080.0000.109
rowQ0.0200.0040.025
selectChannels0.0520.0000.053
selectSome0.0000.0000.001
strbreak0.0000.0000.001
subListExtract1.1320.0081.142
testBioCConnection0.0080.0080.222
updateOldESet0.0000.0000.001
validMsg0.0040.0000.001