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BioC 3.5: CHECK report for Biobase on malbec2

This page was generated on 2017-10-18 14:12:13 -0400 (Wed, 18 Oct 2017).

Package 111/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.36.2
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/Biobase
Branch: RELEASE_3_5
Last Commit: 15f5091
Last Changed Date: 2017-05-02 18:47:56 -0400 (Tue, 02 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biobase
Version: 2.36.2
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.36.2.tar.gz
StartedAt: 2017-10-17 21:31:27 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:32:40 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 73.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.36.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Biobase.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.36.2’
* 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-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rinit.c -o Rinit.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c envir.c -o envir.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matchpt.c -o matchpt.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rowMedians.c -o rowMedians.o
gcc -I/home/biocbuild/bbs-3.5-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-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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
Aggregate0.0240.0040.029
ScalarObject-class0.0120.0000.008
addVig2Menu0.0000.0000.001
anyMissing0.0000.0000.002
cache0.0000.0000.003
channel0.2720.0000.271
channelNames0.1040.0000.103
class.AnnotatedDataFrame0.0280.0040.031
class.ExpressionSet0.2600.0000.261
class.MIAxE0.0160.0000.014
class.MultiSet0.0160.0000.019
class.NChannelSet0.1320.0000.134
class.Versioned0.0440.0000.043
class.VersionedBiobase0.0160.0000.017
class.Versions0.0080.0000.009
class.VersionsNull0.0000.0000.001
class.container0.0040.0000.002
class.eSet0.0560.0000.057
classVersion0.0040.0000.004
contents0.0000.0000.001
copyEnv0.0160.0000.016
copySubstitute0.0680.0000.069
createPackage0.0080.0000.005
data.aaMap0.0000.0000.001
data.geneData0.0280.0000.026
data.reporter0.0000.0000.001
data.sample.ExpressionSet0.0120.0000.013
data.sample.MultiSet0.0040.0000.004
dumpPackTxt0.0040.0000.014
esApply0.9800.0000.981
getPkgVigs0.0080.0000.096
isCurrent0.0200.0000.022
isUnique0.0000.0000.001
isVersioned0.0120.0000.009
lcSuffix0.0280.0000.027
listLen0.0000.0000.001
makeDataPackage0.0800.0040.088
matchpt0.0160.0000.019
multiassign0.0120.0000.014
note000
openPDF000
openVignette000
package.version0.0000.0000.001
read.AnnotatedDataFrame0.0120.0000.010
read.MIAME0.0280.0000.026
readExpressionSet0.0600.0000.061
reverseSplit0.0000.0000.001
rowMedians0.10.00.1
rowQ0.0160.0000.015
selectChannels0.0280.0040.030
selectSome0.0000.0000.001
strbreak0.0200.0000.018
subListExtract0.6480.0080.659
testBioCConnection0.0120.0000.305
updateOldESet0.0000.0000.001
validMsg0.0040.0000.001