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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 868/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goProfiles 1.67.0  (landing page)
Alex Sanchez
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/goProfiles
git_branch: devel
git_last_commit: a95e396
git_last_commit_date: 2024-04-30 10:18:01 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for goProfiles on kjohnson1

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.

raw results


Summary

Package: goProfiles
Version: 1.67.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:goProfiles.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings goProfiles_1.67.0.tar.gz
StartedAt: 2024-06-10 21:18:50 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 21:22:03 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 192.4 seconds
RetCode: 0
Status:   OK  
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:goProfiles.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings goProfiles_1.67.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/goProfiles.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goProfiles/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goProfiles’ version ‘1.67.0’
* 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 code 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 ... 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 sizes of PDF files under ‘inst/doc’ ... 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     21.168  0.363  21.601
equivalentGOProfiles 13.175  0.224  13.489
fisherGOProfiles      6.350  0.099   6.474
mergeProfilesLists    5.710  0.109   5.840
plotProfiles          5.314  0.095   5.430
printProfiles         5.260  0.093   5.373
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/goProfiles.Rcheck/00check.log’
for details.


Installation output

goProfiles.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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
CD4ids0.0030.0030.005
GOTermsList000
basicProfile3.9150.1074.055
compSummary0.0010.0000.001
compareGOProfiles4.6480.0734.744
compareGeneLists21.168 0.36321.601
compareProfilesLists0.0000.0000.001
contractedProfile1.9360.0351.991
conversionFunctions0.0360.0060.042
drosophila0.0030.0030.004
equivClust0.0000.0000.001
equivClust2pdf0.0180.0060.024
equivSummary000
equivalentGOProfiles13.175 0.22413.489
expandedLevel1.1120.0211.138
expandedProfile0.8990.0200.926
fisherGOProfiles6.3500.0996.474
fitGOProfile000
hugoIds0.0170.0020.020
iterEquivClust0.0000.0000.001
mergeProfilesLists5.7100.1095.840
ngenes1.9880.0412.036
omimIds0.0080.0020.010
plotProfiles5.3140.0955.430
printProfiles5.2600.0935.373
prostateIds0.0060.0020.008