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This page was generated on 2024-03-04 11:37:21 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 749/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FoldGO 1.20.0  (landing page)
Daniil Wiebe
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/FoldGO
git_branch: RELEASE_3_18
git_last_commit: 7de3762
git_last_commit_date: 2023-10-24 11:07:52 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for FoldGO on lconway


To the developers/maintainers of the FoldGO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FoldGO.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: FoldGO
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FoldGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FoldGO_1.20.0.tar.gz
StartedAt: 2024-03-03 20:41:05 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 20:43:52 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 166.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: FoldGO.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FoldGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FoldGO_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/FoldGO.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FoldGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FoldGO’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ‘FoldGO’ 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 ... OK
* checking Rd files ... WARNING
checkRd: (5) fagroupstopgo_class.Rd:16: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:17: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:18-19: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:20-21: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:22: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:23: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:25: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:26-27: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:28-29: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:30-31: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:32-33: \item in \describe must have non-empty label
checkRd: (5) fagroupstopgo_class.Rd:42: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:21: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:22: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:23: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:24-25: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:26-27: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:35: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:36: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:37: \item in \describe must have non-empty label
checkRd: (5) foldspectest_class.Rd:38: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:19: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:20: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:28: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:29: \item in \describe must have non-empty label
checkRd: (5) gafreader_class.Rd:37-38: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:24-25: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:26: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:27: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:35-36: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:37-38: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:39: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:40: \item in \describe must have non-empty label
checkRd: (5) genegroups_class.Rd:41: \item in \describe must have non-empty label
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
fagroupstopgo_class          6.459  0.230   6.736
plot-FoldSpecTest-ANY-method 5.299  0.058   5.551
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/FoldGO.Rcheck/00check.log’
for details.



Installation output

FoldGO.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FoldGO
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘FoldGO’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

** inst
** byte-compile and prepare package for lazy loading
in method for ‘getAnnotation’ with signature ‘"MgsaSets"’: no definition for class “MgsaSets”
** 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 (FoldGO)

Tests output


Example timings

FoldGO.Rcheck/FoldGO-Ex.timings

nameusersystemelapsed
examdata_bg0.0020.0010.004
examdata_degs0.0000.0010.002
examdata_objs0.0010.0020.004
fagroupstopgo_class6.4590.2306.736
foldspectest_class2.9950.0673.079
gafreader_class2.9620.8103.816
genegroups_class0.0290.0480.077
getAnnotation0.0010.0000.000
getWholeIntName2.8620.0872.969
plot-FoldSpecTest-ANY-method5.2990.0585.551