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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 914/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gypsum 1.1.4  (landing page)
Aaron Lun
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/gypsum
git_branch: devel
git_last_commit: 57c3bc7
git_last_commit_date: 2024-05-31 01:26:41 -0400 (Fri, 31 May 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 gypsum on kjohnson1

To the developers/maintainers of the gypsum package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gypsum.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: gypsum
Version: 1.1.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gypsum.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gypsum_1.1.4.tar.gz
StartedAt: 2024-06-10 21:53:33 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 21:54:46 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 72.8 seconds
RetCode: 0
Status:   OK  
CheckDir: gypsum.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gypsum.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gypsum_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gypsum.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 ‘gypsum/DESCRIPTION’ ... OK
* this is package ‘gypsum’ version ‘1.1.4’
* 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 ‘gypsum’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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/gypsum.Rcheck/00check.log’
for details.


Installation output

gypsum.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘gypsum’ ...
** using staged installation
** R
** 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 (gypsum)

Tests output

gypsum.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gypsum)
> test_check("gypsum")
[ FAIL 0 | WARN 0 | SKIP 13 | PASS 152 ]

══ Skipped tests (13) ══════════════════════════════════════════════════════════
• is.na(gh_token) is TRUE (13): 'test-accessToken.R:5:5', 'test-latest.R:5:5',
  'test-permissions.R:5:5', 'test-probation.R:5:5', 'test-probation.R:28:5',
  'test-quota.R:5:5', 'test-quota.R:23:5', 'test-remove.R:5:5',
  'test-unlockProject.R:5:5', 'test-upload.R:5:5', 'test-upload.R:55:5',
  'test-upload.R:89:5', 'test-upload.R:107:5'

[ FAIL 0 | WARN 0 | SKIP 13 | PASS 152 ]
> 
> proc.time()
   user  system elapsed 
  3.990   0.534  26.741 

Example timings

gypsum.Rcheck/gypsum-Ex.timings

nameusersystemelapsed
abortUpload0.0020.0020.004
accessToken0.0000.0010.000
approveProbation0.0000.0010.001
cacheDirectory0.0000.0010.001
cloneVersion0.0090.0040.015
completeUpload0.0010.0020.003
createProject0.0000.0000.001
fetchLatest0.0460.0080.338
fetchManifest0.0000.0000.001
fetchMetadataDatabase0.0230.0040.907
fetchMetadataSchema0.0010.0000.001
fetchPermissions0.0110.0010.220
fetchQuota0.0100.0010.209
fetchSummary0.0040.0010.006
fetchUsage0.0110.0000.231
formatObjectMetadata0.9820.0291.015
listAssets0.0100.0010.204
listFiles0.0100.0010.199
listProjects000
listVersions0.0110.0010.200
prepareDirectoryUpload0.0030.0030.007
publicS3Config0.0020.0020.005
refreshLatest000
refreshUsage000
rejectProbation0.0000.0000.001
removeAsset000
removeProject0.0000.0010.001
removeVersion0.0010.0000.001
resolveLinks0.0570.0203.360
restUrl0.0010.0000.000
saveFile0.0000.0000.002
saveVersion0.0000.0000.001
searchMetadataText0.6570.0270.692
setPermissions0.0000.0000.001
setQuota0.0000.0000.001
startUpload0.0010.0020.003
unlockProject000
uploadDirectory0.0010.0020.002
uploadFiles0.0010.0020.002
validateMetadata0.4960.0350.484