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CHECK report for mogsa on merida1

This page was generated on 2019-04-16 11:58:31 -0400 (Tue, 16 Apr 2019).

Package 988/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mogsa 1.16.0
Chen Meng
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/mogsa
Branch: RELEASE_3_8
Last Commit: 322a78f
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mogsa
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mogsa_1.16.0.tar.gz
StartedAt: 2019-04-16 01:23:20 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:27:19 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 238.8 seconds
RetCode: 0
Status:  OK 
CheckDir: mogsa.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mogsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mogsa_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/mogsa.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.16.0’
* 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 ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
prepSupMoa   53.677  1.066  56.011
prepGraphite 40.505  1.034  42.196
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mogsa
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘mogsa’ ...
** 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
* DONE (mogsa)

Tests output


Example timings

mogsa.Rcheck/mogsa-Ex.timings

nameusersystemelapsed
GIS0.5900.0320.628
annotate.gs0.4420.0210.464
bootMbpca000
box.gs.feature0.2400.0250.269
combine-methods0.2450.0350.281
decompose.gs.group0.1760.0140.193
decompose.gs.ind0.1650.0170.185
distMoa0.3540.0240.389
getmgsa0.1660.0220.191
matpower0.0010.0000.001
mbpca3.9280.2524.230
mgsa-class0.2340.0280.262
moGap1.5300.0411.582
moa-class0.1230.0080.136
moa0.1590.0140.175
moa.sup-class0.1460.0140.162
moaCoef0.3820.0210.408
moaScore0.4210.0250.457
mogsa-package0.2960.0320.335
mogsa0.3100.0370.357
pairwise.rv0.0150.0010.017
plotGS0.4970.0140.517
prepGraphite40.505 1.03442.196
prepMsigDB0.0050.0000.006
prepSupMoa53.677 1.06656.011
softK0.0010.0010.001
sup.moa0.5550.0550.613
wsvd0.0010.0000.002