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This page was generated on 2022-08-12 13:22:00 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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

CHECK results for primirTSS on palomino3


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? 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 1492/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
primirTSS 1.14.0  (landing page)
Pumin Li
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/primirTSS
git_branch: RELEASE_3_15
git_last_commit: 9d8ddfa
git_last_commit_date: 2022-04-26 11:50:49 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: primirTSS
Version: 1.14.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:primirTSS.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings primirTSS_1.14.0.tar.gz
StartedAt: 2022-08-12 03:37:08 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 03:41:55 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 287.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: primirTSS.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:primirTSS.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings primirTSS_1.14.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/primirTSS.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'primirTSS/DESCRIPTION' ... OK
* this is package 'primirTSS' version '1.14.0'
* 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 '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, 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/primirTSS.Rcheck/00check.log'
for details.



Installation output

primirTSS.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL primirTSS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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_tss0.060.000.07
peak_join0.270.020.28
peak_merge0.040.000.05
plot_primiRNA0.020.000.01
run_primirTSSapp000
trans_cor0.440.011.21