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This page was generated on 2021-09-15 15:05:54 -0400 (Wed, 15 Sep 2021).

CHECK results for categoryCompare on machv2

To the developers/maintainers of the categoryCompare package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/categoryCompare.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 246/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.36.0  (landing page)
Robert M. Flight
Snapshot Date: 2021-09-14 04:50:06 -0400 (Tue, 14 Sep 2021)
git_url: https://git.bioconductor.org/packages/categoryCompare
git_branch: RELEASE_3_13
git_last_commit: 325b381
git_last_commit_date: 2021-05-19 11:52:22 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: categoryCompare
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings categoryCompare_1.36.0.tar.gz
StartedAt: 2021-09-14 17:05:33 -0400 (Tue, 14 Sep 2021)
EndedAt: 2021-09-14 17:09:34 -0400 (Tue, 14 Sep 2021)
EllapsedTime: 241.3 seconds
RetCode: 0
Status:   OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings categoryCompare_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/categoryCompare.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.36.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘categoryCompare’ 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
.ccCompareGO: no visible binding for global variable ‘GOBPPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOMFPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOCCPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOTERM’
.ccCompareGO: no visible binding for global variable ‘Term’
.cytOutNodes: ... may be used in an incorrect context:
  exportImage(filename = fileName, type = "png", network = cwObj, ...)
.getDesc : <anonymous>: no visible global function definition for
  ‘Term’
show,HyperGResultCC: no visible global function definition for
  ‘description’
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM Term description
* 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-3.13-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.



Installation output

categoryCompare.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL categoryCompare
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘categoryCompare’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: ... may be used in an incorrect context 
** 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 (categoryCompare)

Tests output


Example timings

categoryCompare.Rcheck/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class0.6170.0130.630
HyperGParamsCC-class0.0020.0010.002
HyperGResultCC-class0.0020.0010.003
breakEdges-methods0.8310.0130.844
ccCompare0.7130.0060.719
ccCompareCollection-class0.0010.0010.002
ccCompareResult-class0.0010.0010.002
ccData0.6240.0030.628
ccEnrich0.7070.0050.713
ccEnrichCollection-class1.9200.0341.956
ccEnrichResult-class3.1280.0673.232
ccGeneList-class0.9250.0050.932
ccOptions-class0.0240.0020.027
ccOutCyt-methods0.0000.0000.001
ccSigList-class0.0010.0000.001
cytOutData-methods0.0000.0000.001
cytOutNodes-methods0.0010.0000.001
hyperGTestCC1.1000.0151.116
mergeLists-methods1.0910.0191.111
mergedData-class0.9440.0100.953
minCount2.1570.0422.202
minNodes0.0000.0010.001
pvalueType2.7480.0432.797
show-methods0.0000.0000.001