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This page was generated on 2024-12-23 11:42 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1911/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqArchRplus 1.7.0  (landing page)
Sarvesh Nikumbh
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
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 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  NO, package depends on 'seqArchR' which is not available
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'seqArchR' which is not available
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 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for seqArchRplus on palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqArchRplus.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings seqArchRplus_1.7.0.tar.gz
StartedAt: 2024-12-23 04:48:51 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 04:55:02 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 370.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seqArchRplus.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqArchRplus.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings seqArchRplus_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/seqArchRplus.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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.

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 64.09   3.92   76.71
generate_all_plots              45.72   2.85   48.68
curate_clusters                 10.94   0.84   11.67
per_cluster_annotations         11.23   0.33   12.17
plot_motif_heatmaps2             5.95   1.11    7.20
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/seqArchRplus.Rcheck/00check.log'
for details.


Installation output

seqArchRplus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL seqArchRplus
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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_clusters10.94 0.8411.67
generate_all_plots45.72 2.8548.68
generate_html_report0.020.000.02
handle_tc_from_cage0.790.091.15
iqw_tpm_plots0.640.060.72
order_clusters_iqw0.020.000.01
per_cluster_annotations11.23 0.3312.17
per_cluster_go_term_enrichments64.09 3.9276.71
per_cluster_seqlogos2.390.172.56
per_cluster_strand_dist1.290.021.30
plot_motif_heatmaps1.500.121.64
plot_motif_heatmaps25.951.117.20
seqs_acgt_image2.010.002.02
write_seqArchR_cluster_track_bed0.050.020.08