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This page was generated on 2021-10-15 15:06:47 -0400 (Fri, 15 Oct 2021).

CHECK results for primirTSS on machv2

To the developers/maintainers of the primirTSS package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1430/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
primirTSS 1.10.0  (landing page)
Pumin Li
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/primirTSS
git_branch: RELEASE_3_13
git_last_commit: e9cd880
git_last_commit_date: 2021-05-19 12:37:45 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: primirTSS
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings primirTSS_1.10.0.tar.gz
StartedAt: 2021-10-14 22:31:02 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:36:15 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 313.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: primirTSS.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings primirTSS_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/primirTSS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘primirTSS/DESCRIPTION’ ... OK
* this is package ‘primirTSS’ version ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 R 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 in ‘inst/doc’ ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/primirTSS.Rcheck/00check.log’
for details.



Installation output

primirTSS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL primirTSS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘primirTSS’ ...
** 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 (primirTSS)

Tests output


Example timings

primirTSS.Rcheck/primirTSS-Ex.timings

nameusersystemelapsed
find_tss0.0570.0020.060
peak_join0.5000.0080.509
peak_merge0.1110.0010.112
plot_primiRNA0.0260.0000.027
run_primirTSSapp0.0000.0000.001
trans_cor0.5020.0120.514