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CHECK report for deco on merida2

This page was generated on 2019-04-09 13:38:39 -0400 (Tue, 09 Apr 2019).

Package 391/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deco 0.99.56
Francisco Jose Campos Laborie
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/deco
Branch: master
Last Commit: 41706e8
Last Changed Date: 2019-04-04 04:36:04 -0400 (Thu, 04 Apr 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: deco
Version: 0.99.56
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:deco.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings deco_0.99.56.tar.gz
StartedAt: 2019-04-09 00:19:26 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:23:03 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 216.8 seconds
RetCode: 0
Status:  OK 
CheckDir: deco.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:deco.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings deco_0.99.56.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/deco.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deco/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deco’ version ‘0.99.56’
* 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 ‘deco’ 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 ... NOTE
plotAssociationH: no visible binding for global variable ‘Subclasses’
plotAssociationH: no visible binding for global variable ‘h.statistic’
plotAssociationH: no visible binding for global variable ‘input.info’
plotAssociationH: no visible binding for global variable
  ‘DECO.subclasses’
plotAssociationH: no visible binding for global variable ‘Samples’
plotAssociationH: no visible binding for global variable ‘Features’
plotGainingH: no visible binding for global variable ‘omic.data’
plotGainingH: no visible binding for global variable ‘h.statistic’
plotGainingH: no visible binding for global variable ‘ranking’
Undefined global functions or variables:
  DECO.subclasses Features Samples Subclasses h.statistic input.info
  omic.data ranking
* 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
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/deco.Rcheck/00check.log’
for details.



Installation output

deco.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL deco
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘deco’ ...
** 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 (deco)

Tests output


Example timings

deco.Rcheck/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.2800.0190.301
AnnotateDECO0.1570.0080.166
NSCAcluster1.8990.7532.680
deco-class0.0020.0010.002
deco-package0.2250.0130.240
decoNSCA0.1850.0170.202
decoRDA0.2000.0080.210
decoReport0.1760.0090.184
featureTable0.1610.0080.171
plotAssociationH3.8280.0713.921
plotDECOProfile0.1430.0090.152
plotGainingH1.7140.0151.735
plotHeatmapH0.1520.0060.158