BioC 3.3: CHECK report for Biobase on linux2.bioconductor.org
This page was generated on 2015-10-27 12:11:20 -0400 (Tue, 27 Oct 2015).
Biobase 2.31.0 Bioconductor Package Maintainer
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  |
Summary
Package: Biobase |
Version: 2.31.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.31.0.tar.gz |
StartedAt: 2015-10-27 02:00:19 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 02:01:32 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 73.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Biobase.Rcheck |
Warnings: 0 |
Command output
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### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Biobase_2.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.31.0’
* 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 ... [5s/5s] 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 ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [17s/17s]
Running ‘test-rowMedians.R’ [18s/18s]
[35s/35s] 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 -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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:
name | user | system | elapsed
|
Aggregate | 0.006 | 0.000 | 0.006 |
|
ScalarObject-class | 0.008 | 0.000 | 0.008 |
|
addVig2Menu | 0.001 | 0.000 | 0.001 |
|
anyMissing | 0.001 | 0.000 | 0.002 |
|
cache | 0.003 | 0.000 | 0.003 |
|
channel | 0.079 | 0.000 | 0.078 |
|
channelNames | 0.04 | 0.00 | 0.04 |
|
class.AnnotatedDataFrame | 0.022 | 0.000 | 0.021 |
|
class.ExpressionSet | 0.155 | 0.004 | 0.159 |
|
class.MIAxE | 0.014 | 0.000 | 0.014 |
|
class.MultiSet | 0.022 | 0.000 | 0.022 |
|
class.NChannelSet | 0.122 | 0.000 | 0.122 |
|
class.Versioned | 0.04 | 0.00 | 0.04 |
|
class.VersionedBiobase | 0.018 | 0.004 | 0.022 |
|
class.Versions | 0.011 | 0.000 | 0.011 |
|
class.VersionsNull | 0.001 | 0.000 | 0.001 |
|
class.container | 0.003 | 0.000 | 0.002 |
|
class.eSet | 0.065 | 0.000 | 0.064 |
|
classVersion | 0.003 | 0.000 | 0.003 |
|
contents | 0.001 | 0.000 | 0.001 |
|
copyEnv | 0.001 | 0.000 | 0.000 |
|
copySubstitute | 0.008 | 0.000 | 0.008 |
|
createPackage | 0.000 | 0.004 | 0.005 |
|
data.aaMap | 0.002 | 0.000 | 0.002 |
|
data.geneData | 0.066 | 0.000 | 0.066 |
|
data.reporter | 0.001 | 0.000 | 0.001 |
|
data.sample.ExpressionSet | 0.011 | 0.000 | 0.011 |
|
data.sample.MultiSet | 0.005 | 0.000 | 0.004 |
|
dumpPackTxt | 0.002 | 0.000 | 0.008 |
|
esApply | 0.986 | 0.000 | 0.986 |
|
getPkgVigs | 0.003 | 0.004 | 0.014 |
|
isCurrent | 0.027 | 0.000 | 0.027 |
|
isUnique | 0.001 | 0.000 | 0.000 |
|
isVersioned | 0.009 | 0.000 | 0.009 |
|
lcSuffix | 0.002 | 0.000 | 0.002 |
|
listLen | 0.001 | 0.000 | 0.000 |
|
makeDataPackage | 0.057 | 0.000 | 0.057 |
|
matchpt | 0.004 | 0.000 | 0.004 |
|
multiassign | 0.001 | 0.000 | 0.001 |
|
note | 0.000 | 0.000 | 0.001 |
|
openPDF | 0.001 | 0.000 | 0.001 |
|
openVignette | 0.001 | 0.000 | 0.000 |
|
package.version | 0.001 | 0.004 | 0.001 |
|
read.AnnotatedDataFrame | 0.007 | 0.000 | 0.010 |
|
read.MIAME | 0.002 | 0.000 | 0.002 |
|
readExpressionSet | 0.045 | 0.000 | 0.045 |
|
reverseSplit | 0.000 | 0.000 | 0.001 |
|
rowMedians | 0.083 | 0.000 | 0.085 |
|
rowQ | 0.015 | 0.000 | 0.015 |
|
selectChannels | 0.036 | 0.000 | 0.037 |
|
selectSome | 0.001 | 0.000 | 0.000 |
|
strbreak | 0.001 | 0.000 | 0.001 |
|
subListExtract | 0.679 | 0.008 | 0.686 |
|
testBioCConnection | 0.008 | 0.000 | 0.032 |
|
updateOldESet | 0 | 0 | 0 |
|
validMsg | 0 | 0 | 0 |
|