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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 1590/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
primirTSS 1.24.0  (landing page)
Pumin Li
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/primirTSS
git_branch: RELEASE_3_20
git_last_commit: 4320ad5
git_last_commit_date: 2024-10-29 10:31:09 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation


CHECK results for primirTSS on merida1

To the developers/maintainers of the primirTSS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/primirTSS.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: primirTSS
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings primirTSS_1.24.0.tar.gz
StartedAt: 2024-12-20 07:51:14 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 08:00:03 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 529.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: primirTSS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings primirTSS_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/primirTSS.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 ‘primirTSS/DESCRIPTION’ ... OK
* this is package ‘primirTSS’ version ‘1.24.0’
* 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 ‘primirTSS’ 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'magrittr'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check_DHS_df: no visible binding for global variable ‘can_tss’
check_DHS_df: no visible binding for global variable ‘new_info’
check_DHS_s: no visible binding for global variable ‘dhs_p1’
check_DHS_s: no visible binding for global variable ‘dhs_p2’
eponine_score: no visible binding for global variable ‘previous’
eponine_score: no visible binding for global variable
  ‘histone_p1_flank’
eponine_score: no visible binding for global variable
  ‘histone_p2_flank’
eponine_score: no visible binding for global variable ‘tss_p1’
eponine_score: no visible binding for global variable ‘tss_p2’
find_nearest_peak: no visible binding for global variable ‘mir_name’
find_nearest_peak: no visible binding for global variable ‘start1’
find_nearest_peak: no visible binding for global variable ‘end1’
mir_tf: no visible binding for global variable ‘arrow’
mir_tf: no visible binding for global variable ‘seqname’
mir_tf: no visible binding for global variable ‘TF’
mir_tf: no visible binding for global variable ‘TF_class’
phast_score: no visible binding for global variable ‘loci’
phast_score: no visible binding for global variable ‘eponine_rank’
phast_score: no visible binding for global variable ‘phast_rank’
phast_score: no visible binding for global variable ‘e_p_rank’
phast_score_plot: no visible binding for global variable ‘loci’
plot_primiRNA_track: no visible binding for global variable
  ‘predicted_tss’
plot_primiRNA_track: no visible binding for global variable
  ‘symbol_name’
plot_primiRNA_track: no visible binding for global variable
  ‘stem_loop_p1’
plot_primiRNA_track: no visible binding for global variable
  ‘stem_loop_p2’
plot_primiRNA_track: no visible binding for global variable ‘gene_id’
plot_primiRNA_track: no visible binding for global variable ‘gene_p1’
plot_primiRNA_track: no visible binding for global variable ‘gene_p2’
plot_primiRNA_track: no visible binding for global variable ‘tss_p1’
plot_primiRNA_track: no visible binding for global variable ‘tss_p2’
require_fa: no visible binding for global variable ‘arrow’
tss_filter: no visible binding for global variable ‘gene_id’
tss_filter: no visible binding for global variable ‘new_info’
tss_filter: no visible binding for global variable ‘predicted_tss’
tss_filter: no visible binding for global variable ‘tss_type’
Undefined global functions or variables:
  TF TF_class arrow can_tss dhs_p1 dhs_p2 e_p_rank end1 eponine_rank
  gene_id gene_p1 gene_p2 histone_p1_flank histone_p2_flank loci
  mir_name new_info phast_rank predicted_tss previous seqname start1
  stem_loop_p1 stem_loop_p2 symbol_name tss_p1 tss_p2 tss_type
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/primirTSS.Rcheck/00check.log’
for details.


Installation output

primirTSS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘primirTSS’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg38’
** testing if installed package keeps a record of temporary installation path
* DONE (primirTSS)

Tests output


Example timings

primirTSS.Rcheck/primirTSS-Ex.timings

nameusersystemelapsed
find_tss0.0930.0080.105
peak_join0.8000.0190.859
peak_merge0.1420.0030.161
plot_primiRNA0.0300.0010.031
run_primirTSSapp0.0000.0010.000
trans_cor0.5010.0300.560