Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2023-04-12 11:05:14 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


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 1519/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
primirTSS 1.16.0  (landing page)
Pumin Li
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/primirTSS
git_branch: RELEASE_3_16
git_last_commit: 62bfcf3
git_last_commit_date: 2022-11-01 11:18:23 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: primirTSS
Version: 1.16.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings primirTSS_1.16.0.tar.gz
StartedAt: 2023-04-10 23:03:03 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:08:58 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 355.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: primirTSS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:primirTSS.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings primirTSS_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/primirTSS.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘primirTSS/DESCRIPTION’ ... OK
* this is package ‘primirTSS’ version ‘1.16.0’
* 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 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 loading without being on the library search path ... 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 ...
  ‘primirTSS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/primirTSS.Rcheck/00check.log’
for details.



Installation output

primirTSS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL primirTSS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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_tss0.050.000.05
peak_join0.3270.0630.391
peak_merge0.0590.0080.067
plot_primiRNA0.0080.0080.016
run_primirTSSapp000
trans_cor0.3120.0080.320