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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1639/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R4RNA 1.35.0  (landing page)
Daniel Lai
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/R4RNA
git_branch: devel
git_last_commit: 50cd94f
git_last_commit_date: 2024-10-29 10:05:04 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for R4RNA on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: R4RNA
Version: 1.35.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings R4RNA_1.35.0.tar.gz
StartedAt: 2024-12-23 11:04:57 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 11:06:26 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 89.1 seconds
RetCode: 0
Status:   OK  
CheckDir: R4RNA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:R4RNA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings R4RNA_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/R4RNA.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘R4RNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘R4RNA’ version ‘1.35.0’
* 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 code 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 ... 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 ... NOTE
checkRd: (-1) readStructure.Rd:40: Lost braces; missing escapes or markup?
    40 |     pairs.  Valid brackets are (, {, [, <, A, B, C, D matched with ), }, ], >,
       |                                   ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/R4RNA.Rcheck/00check.log’
for details.


Installation output

R4RNA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL R4RNA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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-package1.7110.0601.777
alignmentStatistics0.5590.0040.564
as.helix0.0020.0000.002
basepairFrequency0.0070.0000.007
blankPlot0.0560.0000.056
colourHelices0.3150.0040.320
expandCollapseHelix0.010.000.01
logicalHelix0.5150.0160.532
logseq000
plotCovariance0.6320.0040.638
plotHelix0.6530.0280.682
readStructure0.0320.0040.036
structureMismatchScore0.0040.0000.003
unknottedGroups0.020.000.02
viennaToHelix0.0620.0040.067
writeHelix0.0020.0000.003