Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:07 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 1965/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Sarvesh Nikumbh
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: seqArchRplus |
Version: 1.9.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:seqArchRplus.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqArchRplus_1.9.2.tar.gz |
StartedAt: 2025-10-10 13:28:31 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 13:36:45 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 494.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: seqArchRplus.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:seqArchRplus.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqArchRplus_1.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/seqArchRplus.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqArchRplus/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqArchRplus’ version ‘1.9.2’ * 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 loading without being on the library search path ... 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(s) in Rd file 'generate_all_plots.Rd': ‘[CAGEr]{clusterCTSS}’ Non-topic package-anchored link(s) in Rd file 'handle_tc_from_cage.Rd': ‘[CAGEr]{tagClusters}’ Non-topic package-anchored link(s) in Rd file 'per_cluster_annotations.Rd': ‘[CAGEr]{tagClusters}’ Non-topic package-anchored link(s) in Rd file 'per_cluster_go_term_enrichments.Rd': ‘[CAGEr]{tagClusters}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: seqArchRplus.Rd: prepare_data_from_FASTA, get_one_hot_encoded_seqs, plot_arch_for_clusters, plot_ggseqlogo_of_seqs, viz_bas_vec, viz_seqs_acgt_mat, viz_pwm Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 generate_all_plots 53.058 1.326 76.004 per_cluster_go_term_enrichments 53.472 0.681 76.553 curate_clusters 14.689 0.374 22.284 per_cluster_annotations 11.353 0.078 14.820 plot_motif_heatmaps2 7.346 0.188 11.921 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/seqArchRplus.Rcheck/00check.log’ for details.
seqArchRplus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL seqArchRplus ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘seqArchRplus’ ... ** this is package ‘seqArchRplus’ version ‘1.9.2’ ** 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 Warning in fun(libname, pkgname) : Package 'seqArchRplus' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'seqArchRplus' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package keeps a record of temporary installation path * DONE (seqArchRplus)
seqArchRplus.Rcheck/seqArchRplus-Ex.timings
name | user | system | elapsed | |
curate_clusters | 14.689 | 0.374 | 22.284 | |
generate_all_plots | 53.058 | 1.326 | 76.004 | |
generate_html_report | 0.006 | 0.000 | 0.011 | |
handle_tc_from_cage | 0.898 | 0.091 | 3.574 | |
iqw_tpm_plots | 1.179 | 0.016 | 1.330 | |
order_clusters_iqw | 0.019 | 0.000 | 0.027 | |
per_cluster_annotations | 11.353 | 0.078 | 14.820 | |
per_cluster_go_term_enrichments | 53.472 | 0.681 | 76.553 | |
per_cluster_seqlogos | 3.563 | 0.023 | 3.888 | |
per_cluster_strand_dist | 2.225 | 0.044 | 2.994 | |
plot_motif_heatmaps | 1.585 | 0.016 | 1.777 | |
plot_motif_heatmaps2 | 7.346 | 0.188 | 11.921 | |
seqs_acgt_image | 0.319 | 0.000 | 0.636 | |
write_seqArchR_cluster_track_bed | 0.051 | 0.000 | 0.063 | |