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This page was generated on 2023-04-12 11:06:31 -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 Ularcirc on lconway


To the developers/maintainers of the Ularcirc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Ularcirc.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 2119/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ularcirc 1.16.0  (landing page)
David Humphreys
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/Ularcirc
git_branch: RELEASE_3_16
git_last_commit: c4f780d
git_last_commit_date: 2022-11-01 11:17:58 -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: Ularcirc
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Ularcirc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Ularcirc_1.16.0.tar.gz
StartedAt: 2023-04-10 23:14:58 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:16:31 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 93.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Ularcirc.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Ularcirc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Ularcirc_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/Ularcirc.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ularcirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ularcirc’ 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 ‘Ularcirc’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘DT’ ‘GenomeInfoDb’ ‘GenomeInfoDbData’ ‘Organism.dplyr’ ‘ggplot2’
  ‘ggrepel’ ‘mirbase.db’ ‘moments’ ‘shinyFiles’ ‘shinydashboard’
  ‘shinyjs’ ‘yaml’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FilterChimericJuncs: no visible global function definition for
  ‘Filter_by_Data_Set’
FilterChimericJuncs: no visible binding for global variable
  ‘strandDonor’
FilterChimericJuncs: no visible binding for global variable
  ‘startDonor’
FilterChimericJuncs: no visible binding for global variable
  ‘startAcceptor’
Junction_Sequence_from_Genome: no visible global function definition
  for ‘extractGenomeSequence’
SelectUniqueJunctions : filtersteps: no visible global function
  definition for ‘.’
SelectUniqueJunctions: no visible binding for global variable
  ‘BSjuncName’
SelectUniqueJunctions: no visible binding for global variable
  ‘JuncType’
SelectUniqueJunctions: no visible binding for global variable
  ‘strandDonor’
loadSTAR_chimeric: no visible binding for global variable
  ‘..returnColIdx’
Undefined global functions or variables:
  . ..returnColIdx BSjuncName Filter_by_Data_Set JuncType
  extractGenomeSequence startAcceptor startDonor strandDonor
* 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 ... WARNING
Undocumented arguments in documentation object 'Junction_Sequence_from_Genome'
  ‘SelectUniqueJunct_Value’
Documented arguments not in \usage in documentation object 'Junction_Sequence_from_Genome':
  ‘SelectUniqueJunct_value’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Compatible_Annotation_DBs 8.012  0.396    8.43
* 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-3.16-bioc/meat/Ularcirc.Rcheck/00check.log’
for details.



Installation output

Ularcirc.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘Ularcirc’ ...
** 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 (Ularcirc)

Tests output


Example timings

Ularcirc.Rcheck/Ularcirc-Ex.timings

nameusersystemelapsed
BSJ_details0.0010.0010.002
Compatible_Annotation_DBs8.0120.3968.430
FilterChimericJuncs0.2280.0120.243
Ularcirc000
bsj_fastq_generate0.0440.0010.046
bsj_to_circRNA_sequence2.5950.0792.686
chimericStats0.0430.0050.049
plot_AllJunctions1.3440.0501.399