Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1926/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqArchRplus 1.6.0 (landing page) Sarvesh Nikumbh
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the seqArchRplus package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqArchRplus.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: seqArchRplus |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqArchRplus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqArchRplus_1.6.0.tar.gz |
StartedAt: 2024-12-20 09:31:57 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 09:42:00 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 603.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: seqArchRplus.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqArchRplus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqArchRplus_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqArchRplus.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqArchRplus/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqArchRplus’ version ‘1.6.0’ * 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 ‘seqArchRplus’ 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 whether startup messages can be suppressed ... 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 ... WARNING Missing link or links in Rd file 'generate_all_plots.Rd': ‘[CAGEr]{clusterCTSS}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 per_cluster_go_term_enrichments 79.041 3.175 88.860 generate_all_plots 74.339 3.055 82.314 per_cluster_annotations 18.704 0.325 19.728 curate_clusters 16.918 0.398 18.011 plot_motif_heatmaps2 11.197 0.356 11.855 * 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 WARNING See ‘/Users/biocbuild/bbs-3.20-bioc/meat/seqArchRplus.Rcheck/00check.log’ for details.
seqArchRplus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqArchRplus ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘seqArchRplus’ ... ** 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 (seqArchRplus)
seqArchRplus.Rcheck/seqArchRplus-Ex.timings
name | user | system | elapsed | |
curate_clusters | 16.918 | 0.398 | 18.011 | |
generate_all_plots | 74.339 | 3.055 | 82.314 | |
generate_html_report | 0.019 | 0.004 | 0.023 | |
handle_tc_from_cage | 1.445 | 0.281 | 1.922 | |
iqw_tpm_plots | 1.245 | 0.146 | 1.455 | |
order_clusters_iqw | 0.032 | 0.006 | 0.037 | |
per_cluster_annotations | 18.704 | 0.325 | 19.728 | |
per_cluster_go_term_enrichments | 79.041 | 3.175 | 88.860 | |
per_cluster_seqlogos | 4.046 | 0.064 | 4.463 | |
per_cluster_strand_dist | 1.968 | 0.017 | 2.121 | |
plot_motif_heatmaps | 1.943 | 0.099 | 2.225 | |
plot_motif_heatmaps2 | 11.197 | 0.356 | 11.855 | |
seqs_acgt_image | 0.493 | 0.017 | 0.560 | |
write_seqArchR_cluster_track_bed | 0.087 | 0.009 | 0.106 | |