Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:43 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 920/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gypsum 1.1.6 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: gypsum |
Version: 1.1.6 |
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_1.1.6.tar.gz |
StartedAt: 2024-08-26 21:01:48 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 21:03:05 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 76.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gypsum.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.1.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gypsum.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gypsum/DESCRIPTION’ ... OK * this is package ‘gypsum’ version ‘1.1.6’ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed fetchLatest 0.044 0.009 6.597 * 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.
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-x86_64/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)
gypsum.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 252 ] ══ 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 252 ] > > proc.time() user system elapsed 4.758 0.639 18.340
gypsum.Rcheck/gypsum-Ex.timings
name | user | system | elapsed | |
abortUpload | 0.001 | 0.002 | 0.003 | |
accessToken | 0.000 | 0.000 | 0.001 | |
approveProbation | 0.001 | 0.001 | 0.002 | |
cacheDirectory | 0.000 | 0.000 | 0.001 | |
cloneVersion | 0.009 | 0.005 | 0.021 | |
completeUpload | 0.001 | 0.001 | 0.003 | |
createProject | 0 | 0 | 0 | |
fetchLatest | 0.044 | 0.009 | 6.597 | |
fetchManifest | 0.001 | 0.000 | 0.001 | |
fetchMetadataDatabase | 0.021 | 0.005 | 0.493 | |
fetchMetadataSchema | 0.000 | 0.001 | 0.002 | |
fetchPermissions | 0.012 | 0.001 | 0.155 | |
fetchQuota | 0.011 | 0.001 | 0.143 | |
fetchSummary | 0.004 | 0.002 | 0.006 | |
fetchUsage | 0.011 | 0.001 | 0.159 | |
formatObjectMetadata | 1.112 | 0.045 | 1.164 | |
listAssets | 0.010 | 0.002 | 0.153 | |
listFiles | 0.010 | 0.001 | 0.150 | |
listProjects | 0.000 | 0.000 | 0.001 | |
listVersions | 0.012 | 0.002 | 0.138 | |
prepareDirectoryUpload | 0.004 | 0.003 | 0.007 | |
publicS3Config | 0.002 | 0.001 | 0.004 | |
refreshLatest | 0 | 0 | 0 | |
refreshUsage | 0.000 | 0.000 | 0.001 | |
rejectProbation | 0 | 0 | 0 | |
removeAsset | 0 | 0 | 0 | |
removeProject | 0.000 | 0.000 | 0.001 | |
removeVersion | 0.001 | 0.000 | 0.000 | |
resolveLinks | 0.054 | 0.017 | 1.091 | |
restUrl | 0 | 0 | 0 | |
saveFile | 0.000 | 0.000 | 0.002 | |
saveVersion | 0.001 | 0.000 | 0.002 | |
searchMetadata | 0.651 | 0.040 | 0.706 | |
setPermissions | 0 | 0 | 0 | |
setQuota | 0.000 | 0.001 | 0.001 | |
startUpload | 0.001 | 0.002 | 0.003 | |
translateTextQuery | 0.052 | 0.009 | 0.062 | |
unlockProject | 0 | 0 | 0 | |
uploadDirectory | 0.001 | 0.002 | 0.002 | |
uploadFiles | 0.001 | 0.002 | 0.003 | |
validateMetadata | 0.440 | 0.044 | 0.447 | |