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This page was generated on 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1894/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqArchRplus 1.5.0  (landing page)
Sarvesh Nikumbh
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/seqArchRplus
git_branch: devel
git_last_commit: 67eccab
git_last_commit_date: 2024-04-30 11:46:19 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows 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 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for seqArchRplus on nebbiolo2

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: 1.5.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqArchRplus.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqArchRplus_1.5.0.tar.gz
StartedAt: 2024-07-24 03:55:15 -0400 (Wed, 24 Jul 2024)
EndedAt: 2024-07-24 04:02:29 -0400 (Wed, 24 Jul 2024)
EllapsedTime: 433.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seqArchRplus.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:seqArchRplus.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings seqArchRplus_1.5.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/seqArchRplus.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘seqArchRplus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqArchRplus’ version ‘1.5.0’
* 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 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 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 43.303  0.823  44.136
generate_all_plots              37.870  1.076  38.959
per_cluster_annotations          9.544  0.080   9.624
curate_clusters                  8.662  0.200   8.863
plot_motif_heatmaps2             6.212  0.260   6.400
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/seqArchRplus.Rcheck/00check.log’
for details.


Installation output

seqArchRplus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL seqArchRplus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output


Example timings

seqArchRplus.Rcheck/seqArchRplus-Ex.timings

nameusersystemelapsed
curate_clusters8.6620.2008.863
generate_all_plots37.870 1.07638.959
generate_html_report0.0060.0000.006
handle_tc_from_cage0.6580.0160.766
iqw_tpm_plots0.4420.0000.441
order_clusters_iqw0.0140.0000.014
per_cluster_annotations9.5440.0809.624
per_cluster_go_term_enrichments43.303 0.82344.136
per_cluster_seqlogos1.8100.0001.809
per_cluster_strand_dist0.7940.0200.814
plot_motif_heatmaps1.3870.0121.399
plot_motif_heatmaps26.2120.2606.400
seqs_acgt_image0.2810.0000.282
write_seqArchR_cluster_track_bed0.0380.0000.038