Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:04:44 -0500 (Fri, 03 Dec 2021).

CHECK results for categoryCompare on nebbiolo2

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 251/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.38.0  (landing page)
Robert M. Flight
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/categoryCompare
git_branch: RELEASE_3_14
git_last_commit: 13d544a
git_last_commit_date: 2021-10-26 12:03:05 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: 1.38.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings categoryCompare_1.38.0.tar.gz
StartedAt: 2021-12-02 06:29:21 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:31:56 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 154.8 seconds
RetCode: 0
Status:   OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings categoryCompare_1.38.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/categoryCompare.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.38.0’
* 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 ‘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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.



Installation output

categoryCompare.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL categoryCompare
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-class0.4640.0280.492
HyperGParamsCC-class0.0010.0000.001
HyperGResultCC-class0.0000.0000.001
breakEdges-methods0.4880.0200.509
ccCompare0.5000.0040.504
ccCompareCollection-class0.0010.0000.000
ccCompareResult-class0.0010.0000.000
ccData0.4250.0080.434
ccEnrich0.4230.0120.435
ccEnrichCollection-class1.5230.0401.562
ccEnrichResult-class2.2940.0202.314
ccGeneList-class0.4790.0080.487
ccOptions-class0.0140.0000.015
ccOutCyt-methods000
ccSigList-class0.0010.0000.000
cytOutData-methods0.0000.0000.001
cytOutNodes-methods000
hyperGTestCC0.6590.0120.671
mergeLists-methods0.6970.0120.708
mergedData-class0.5610.0240.585
minCount1.4240.0281.451
minNodes000
pvalueType1.9360.0161.953
show-methods0.0000.0000.001