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This page was generated on 2022-06-24 12:07:19 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for deco on merida1


To the developers/maintainers of the deco package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/deco.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 481/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deco 1.12.0  (landing page)
Francisco Jose Campos Laborie
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/deco
git_branch: RELEASE_3_15
git_last_commit: f398a46
git_last_commit_date: 2022-04-26 11:52:35 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: deco
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deco.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deco_1.12.0.tar.gz
StartedAt: 2022-06-24 01:40:22 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 01:46:46 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 384.2 seconds
RetCode: 0
Status:   OK  
CheckDir: deco.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:deco.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings deco_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/deco.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.12.0’
* 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 ‘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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.analysisType’ ‘.heatplot.2’
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/deco.Rcheck/00check.log’
for details.



Installation output

deco.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL deco
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘deco’ ...
** 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 (deco)

Tests output


Example timings

deco.Rcheck/deco-Ex.timings

nameusersystemelapsed
ALCLdata0.3530.0140.387
AnnotateDECO0.2060.0050.221
NSCAcluster1.4380.9232.545
deco-class0.0020.0000.002
deco-package0.9250.0140.988
decoNSCA0.9550.0161.014
decoRDA0.2610.0060.279
decoReport0.2110.0060.230
featureTable0.2110.0060.226
plotAssociationH4.4890.1484.829
plotDECOProfile0.2300.0060.248
plotGainingH2.4680.0752.647
plotHeatmapH0.2370.0090.262