Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-12-07 11:05:23 -0500 (Wed, 07 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4423
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4193
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 categoryCompare on nebbiolo1


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? 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 254/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.43.0  (landing page)
Robert M. Flight
Snapshot Date: 2022-12-06 14:00:17 -0500 (Tue, 06 Dec 2022)
git_url: https://git.bioconductor.org/packages/categoryCompare
git_branch: master
git_last_commit: d82fecd
git_last_commit_date: 2022-11-01 11:06:57 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: categoryCompare
Version: 1.43.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings categoryCompare_1.43.0.tar.gz
StartedAt: 2022-12-06 19:33:56 -0500 (Tue, 06 Dec 2022)
EndedAt: 2022-12-06 19:39:09 -0500 (Tue, 06 Dec 2022)
EllapsedTime: 312.6 seconds
RetCode: 0
Status:   OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings categoryCompare_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/categoryCompare.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.43.0’
* 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 ...
  ‘categoryCompare_vignette.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.



Installation output

categoryCompare.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL categoryCompare
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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-class0.4370.0200.457
HyperGParamsCC-class0.0010.0000.001
HyperGResultCC-class0.0000.0010.001
breakEdges-methods0.5950.0140.610
ccCompare0.4740.0070.482
ccCompareCollection-class0.0010.0000.001
ccCompareResult-class0.0010.0000.001
ccData1.0780.0681.146
ccEnrich0.4590.0050.463
ccEnrichCollection-class1.1650.0351.202
ccEnrichResult-class2.4000.0242.424
ccGeneList-class0.5180.0040.523
ccOptions-class0.0180.0010.019
ccOutCyt-methods000
ccSigList-class0.0000.0000.001
cytOutData-methods0.0000.0000.001
cytOutNodes-methods0.0000.0000.001
hyperGTestCC0.6850.0150.701
mergeLists-methods0.7070.0320.740
mergedData-class0.6030.0230.628
minCount1.5120.0281.540
minNodes0.0010.0000.000
pvalueType2.0060.1202.125
show-methods000