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CHECK report for mogsa on malbec2

This page was generated on 2019-04-09 11:42:05 -0400 (Tue, 09 Apr 2019).

Package 1016/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mogsa 1.17.5
Chen Meng
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/mogsa
Branch: master
Last Commit: 4199ff7
Last Changed Date: 2019-02-13 10:12:36 -0400 (Wed, 13 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: mogsa
Version: 1.17.5
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings mogsa_1.17.5.tar.gz
StartedAt: 2019-04-09 02:07:51 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:12:02 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 250.8 seconds
RetCode: 0
Status:  OK 
CheckDir: mogsa.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:mogsa.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings mogsa_1.17.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/mogsa.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mogsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mogsa’ version ‘1.17.5’
* 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 ‘mogsa’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
prepSupMoa   50.685  0.100  51.467
prepGraphite 47.875  0.605  49.304
* 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


Installation output

mogsa.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL mogsa
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘mogsa’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mogsa)

Tests output


Example timings

mogsa.Rcheck/mogsa-Ex.timings

nameusersystemelapsed
GIS0.5930.0080.610
annotate.gs0.5140.0040.544
bootMbpca000
bootMoa000
box.gs.feature0.2470.0080.255
combine-methods0.2540.0040.260
decompose.gs.group0.1650.0000.167
decompose.gs.ind0.1430.0040.149
distMoa0.7510.0000.762
getmgsa0.1260.0000.129
matpower0.0010.0000.001
mbpca3.6320.0133.685
mgsa-class0.6070.0060.614
moGap3.3260.0123.407
moa-class0.1160.0040.136
moa0.7330.0200.784
moa.sup-class0.1370.0070.145
moaCoef0.4180.0000.422
moaScore0.4180.0030.429
mogsa-package0.6660.0040.703
mogsa0.3900.0000.395
pairwise.rv0.0090.0040.013
plotGS0.1490.0040.154
prepGraphite47.875 0.60549.304
prepMsigDB0.0030.0020.019
prepSupMoa50.685 0.10051.467
softK000
sup.moa0.3880.0080.397
wsvd0.0020.0000.001