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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 2166/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Ularcirc 1.18.0  (landing page)
David Humphreys
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Ularcirc
git_branch: RELEASE_3_17
git_last_commit: 59e062b
git_last_commit_date: 2023-04-25 11:02:25 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for Ularcirc on kjohnson2


To the developers/maintainers of the Ularcirc package:
- 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: Ularcirc
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2023-10-19 08:58:16 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 09:01:46 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 210.3 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Ularcirc.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Ularcirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Ularcirc’ version ‘1.18.0’
* 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 9.600  0.452  17.926
bsj_to_circRNA_sequence   3.596  0.203   6.829
* 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-3.17-bioc-mac-arm64/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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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_details0.0020.0010.003
Compatible_Annotation_DBs 9.600 0.45217.926
FilterChimericJuncs0.1680.0150.311
Ularcirc0.0000.0010.001
bsj_fastq_generate0.0610.0020.108
bsj_to_circRNA_sequence3.5960.2036.829
chimericStats0.0690.0100.135
plot_AllJunctions1.8040.1113.463