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CHECK report for mogsa on machv2

This page was generated on 2020-10-17 11:58:59 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE mogsa PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1117/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mogsa 1.22.1
Chen Meng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/mogsa
Branch: RELEASE_3_11
Last Commit: ab0a8c2
Last Changed Date: 2020-06-04 10:07:27 -0400 (Thu, 04 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mogsa
Version: 1.22.1
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_1.22.1.tar.gz
StartedAt: 2020-10-17 03:12:21 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:15:45 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 204.3 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_1.22.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/mogsa.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.22.1’
* 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
* 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/4.0/Resources/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
GIS0.2960.0330.330
annotate.gs0.2180.0200.239
bootMbpca0.0000.0000.001
bootMoa0.0000.0000.001
box.gs.feature0.3470.0200.367
combine-methods0.6960.0210.717
decompose.gs.group0.2270.0190.247
decompose.gs.ind0.1680.0120.180
distMoa0.3460.0130.358
getmgsa0.1940.0100.204
matpower0.0010.0000.001
mbpca4.6510.1754.831
mgsa-class0.3370.0200.357
moGap2.9780.0523.034
moa-class0.1430.0030.146
moa0.8710.0380.911
moa.sup-class0.1830.0130.195
moaCoef0.4440.0080.452
moaScore0.4540.0150.469
mogsa-package0.3810.0410.422
mogsa0.5170.0180.535
pairwise.rv0.0170.0020.018
plotGS0.2030.0160.219
prepGraphite0.4180.0110.430
prepMsigDB0.0040.0000.004
prepSupMoa3.7120.0483.764
softK000
sup.moa0.9240.0100.935
wsvd0.0010.0010.002