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This page was generated on 2024-03-27 11:37:59 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 1647/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R4RNA 1.30.0  (landing page)
Daniel Lai
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/R4RNA
git_branch: RELEASE_3_18
git_last_commit: ea54eef
git_last_commit_date: 2023-10-24 10:46:12 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for R4RNA on merida1


To the developers/maintainers of the R4RNA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/R4RNA.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: R4RNA
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R4RNA_1.30.0.tar.gz
StartedAt: 2024-03-26 07:12:52 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 07:15:23 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 150.3 seconds
RetCode: 0
Status:   OK  
CheckDir: R4RNA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings R4RNA_1.30.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/R4RNA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R4RNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R4RNA’ version ‘1.30.0’
* 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 ‘R4RNA’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignmentCanonical: no visible global function definition for ‘is’
alignmentConservation: no visible global function definition for ‘is’
alignmentCovariation: no visible global function definition for ‘is’
alignmentPercentGaps: no visible global function definition for ‘is’
arc: no visible global function definition for ‘lines’
baseConservation: no visible global function definition for ‘is’
basepairCanonical: no visible global function definition for ‘is’
basepairConservation: no visible global function definition for ‘is’
basepairCovariation: no visible global function definition for ‘is’
blankPlot: no visible global function definition for ‘par’
blankPlot: no visible global function definition for ‘abline’
colourByCanonical: no visible global function definition for ‘is’
colourByConservation: no visible global function definition for ‘is’
colourByCovariation: no visible global function definition for ‘is’
getBaseColours: no visible global function definition for ‘is’
getCovarianceColours: no visible global function definition for ‘is’
getSequenceColour: no visible global function definition for ‘is’
helixCanonical: no visible global function definition for ‘is’
helixConservation: no visible global function definition for ‘is’
helixCovariation: no visible global function definition for ‘is’
isConflictingHelix: no visible global function definition for
  ‘aggregate’
isDuplicatingHelix: no visible global function definition for
  ‘aggregate’
isOverlappingHelix: no visible global function definition for
  ‘aggregate’
plotArc: no visible global function definition for ‘lines’
plotArrow: no visible global function definition for ‘polygon’
plotCovariance: no visible global function definition for ‘is’
plotCovarianceGrid: no visible global function definition for ‘rect’
plotCovarianceLine: no visible global function definition for
  ‘segments’
plotDoubleCovariance: no visible global function definition for ‘is’
plotDoubleHelix: no visible global function definition for ‘lines’
plotHelix: no visible global function definition for ‘lines’
plotOverlapCovariance: no visible global function definition for ‘is’
plotOverlapHelix: no visible global function definition for ‘lines’
plotScale: no visible global function definition for ‘strheight’
plotScale: no visible global function definition for ‘segments’
plotScale: no visible global function definition for ‘text’
readConnect: no visible global function definition for ‘read.delim’
readHelix: no visible global function definition for ‘read.delim’
structureMismatchScore: no visible global function definition for ‘is’
writeHelix: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline aggregate is lines par polygon read.delim rect segments
  strheight text write.table
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon", "rect",
             "segments", "strheight", "text")
  importFrom("methods", "is")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/R4RNA.Rcheck/00check.log’
for details.



Installation output

R4RNA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL R4RNA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘R4RNA’ ...
** using staged installation
** R
** data
** 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 (R4RNA)

Tests output


Example timings

R4RNA.Rcheck/R4RNA-Ex.timings

nameusersystemelapsed
R4RNA-package2.1130.1952.319
alignmentStatistics0.9380.0160.956
as.helix0.0020.0010.004
basepairFrequency0.0140.0120.026
blankPlot0.0800.0040.084
colourHelices0.5020.0210.525
expandCollapseHelix0.0150.0020.017
logicalHelix0.8590.0330.896
logseq0.0000.0010.001
plotCovariance1.0470.0281.096
plotHelix1.0380.0581.103
readStructure0.0580.0070.065
structureMismatchScore0.0050.0030.008
unknottedGroups0.0360.0080.044
viennaToHelix0.0890.0030.093
writeHelix0.0040.0000.005