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This page was generated on 2025-03-19 11:45 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 1939/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqArchRplus 1.7.0  (landing page)
Sarvesh Nikumbh
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025)
git_url: https://git.bioconductor.org/packages/seqArchRplus
git_branch: devel
git_last_commit: 782da3e
git_last_commit_date: 2024-10-29 11:16:40 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for seqArchRplus on lconway

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.

raw results


Summary

Package: seqArchRplus
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2025-03-18 23:46:23 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 23:51:48 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 325.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seqArchRplus.Rcheck
Warnings: 1

Command output

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### 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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/seqArchRplus.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.7.0’
* 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(s) in Rd file 'generate_all_plots.Rd':
  ‘[CAGEr]{clusterCTSS}’

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
per_cluster_go_term_enrichments 52.272  3.196  56.019
generate_all_plots              38.926  2.398  41.953
per_cluster_annotations         11.180  0.240  11.482
curate_clusters                  8.908  0.274   9.244
plot_motif_heatmaps2             5.376  0.308   5.741
* 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-3.21-bioc/meat/seqArchRplus.Rcheck/00check.log’
for details.


Installation output

seqArchRplus.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘seqArchRplus’ ...
** this is package ‘seqArchRplus’ version ‘1.7.0’
** 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)

Tests output


Example timings

seqArchRplus.Rcheck/seqArchRplus-Ex.timings

nameusersystemelapsed
curate_clusters8.9080.2749.244
generate_all_plots38.926 2.39841.953
generate_html_report0.0120.0020.013
handle_tc_from_cage0.8480.1621.084
iqw_tpm_plots0.5840.0110.600
order_clusters_iqw0.0140.0020.015
per_cluster_annotations11.180 0.24011.482
per_cluster_go_term_enrichments52.272 3.19656.019
per_cluster_seqlogos2.0220.0412.073
per_cluster_strand_dist0.9410.0220.980
plot_motif_heatmaps1.0880.0511.145
plot_motif_heatmaps25.3760.3085.741
seqs_acgt_image0.2940.0180.323
write_seqArchR_cluster_track_bed0.0450.0050.051