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This page was generated on 2023-11-29 11:38:11 -0500 (Wed, 29 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4601
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" 4343
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4368
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" 4253
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

Package 867/2225HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goProfiles 1.65.0  (landing page)
Alex Sanchez
Snapshot Date: 2023-11-28 14:00:17 -0500 (Tue, 28 Nov 2023)
git_url: https://git.bioconductor.org/packages/goProfiles
git_branch: devel
git_last_commit: d89d711
git_last_commit_date: 2023-10-24 09:39:46 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for goProfiles on kunpeng2


To the developers/maintainers of the goProfiles package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/goProfiles.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: goProfiles
Version: 1.65.0
Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:goProfiles.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings goProfiles_1.65.0.tar.gz
StartedAt: 2023-11-29 05:45:42 -0000 (Wed, 29 Nov 2023)
EndedAt: 2023-11-29 05:49:02 -0000 (Wed, 29 Nov 2023)
EllapsedTime: 199.4 seconds
RetCode: 0
Status:   OK  
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:goProfiles.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings goProfiles_1.65.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/goProfiles.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goProfiles/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goProfiles’ version ‘1.65.0’
* 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 ‘goProfiles’ 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 loading without being on the library search path ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) compareGeneLists.Rd:6: Escaped LaTeX specials: \~
checkRd: (-1) compareProfilesLists.Rd:7: Escaped LaTeX specials: \~
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
compareGeneLists     21.940  0.240  22.236
equivalentGOProfiles 14.205  0.096  14.343
fisherGOProfiles      5.964  0.048   6.026
mergeProfilesLists    5.533  0.083   5.630
printProfiles         5.387  0.032   5.430
plotProfiles          5.226  0.020   5.257
* 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-3.19-bioc/meat/goProfiles.Rcheck/00check.log’
for details.



Installation output

goProfiles.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL goProfiles
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘goProfiles’ ...
** 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 (goProfiles)

Tests output


Example timings

goProfiles.Rcheck/goProfiles-Ex.timings

nameusersystemelapsed
CD4ids0.0020.0000.003
GOTermsList0.0000.0000.001
basicProfile3.8500.1074.019
compSummary000
compareGOProfiles4.4890.0804.582
compareGeneLists21.940 0.24022.236
compareProfilesLists000
contractedProfile2.0070.0122.024
conversionFunctions0.0500.0000.051
drosophila0.0020.0000.002
equivClust000
equivClust2pdf0.0210.0040.025
equivSummary0.0010.0000.000
equivalentGOProfiles14.205 0.09614.343
expandedLevel1.5130.0241.541
expandedProfile0.9570.0040.964
fisherGOProfiles5.9640.0486.026
fitGOProfile000
hugoIds0.0130.0020.014
iterEquivClust0.0000.0000.001
mergeProfilesLists5.5330.0835.630
ngenes2.0290.0122.046
omimIds0.0050.0000.006
plotProfiles5.2260.0205.257
printProfiles5.3870.0325.430
prostateIds0.0050.0000.005