Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1953/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
segmentSeq 2.42.0  (landing page)
Samuel Granjeaud
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/segmentSeq
git_branch: RELEASE_3_21
git_last_commit: b06bb70
git_last_commit_date: 2025-04-15 09:46:52 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for segmentSeq on merida1

To the developers/maintainers of the segmentSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmentSeq.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: segmentSeq
Version: 2.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmentSeq_2.42.0.tar.gz
StartedAt: 2025-08-19 11:06:33 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 11:17:36 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 663.3 seconds
RetCode: 0
Status:   OK  
CheckDir: segmentSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmentSeq_2.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/segmentSeq.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.42.0’
* 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 ‘segmentSeq’ 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  averageMethylationRegions.Rd: GRanges-class
  findChunks.Rd: GRanges-class, GRanges
  lociData-class.Rd: countData, countData-class
  methData-class.Rd: countData, countData-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
classifySeg         49.191  0.505  54.739
lociLikelihoods     20.193  0.095  22.321
heuristicSeg        19.747  0.082  21.598
plotGenome          11.571  0.089  12.680
getCounts            6.971  0.023   7.568
normaliseNC          5.589  0.287   6.378
processAD            5.608  0.025   6.077
segData-class        5.542  0.082   6.656
segmentSeq-package   5.587  0.030   6.162
thresholdFinder      5.295  0.196   5.822
readMeths            4.555  0.188   5.213
alignmentData-class  4.685  0.026   5.005
getOverlaps          4.654  0.019   5.078
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.


Installation output

segmentSeq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘segmentSeq’ ...
** this is package ‘segmentSeq’ version ‘2.42.0’
** 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 (segmentSeq)

Tests output


Example timings

segmentSeq.Rcheck/segmentSeq-Ex.timings

nameusersystemelapsed
alignmentData-class4.6850.0265.005
classifySeg49.191 0.50554.739
findChunks4.4380.0204.842
getCounts6.9710.0237.568
getOverlaps4.6540.0195.078
heuristicSeg19.747 0.08221.598
lociLikelihoods20.193 0.09522.321
normaliseNC5.5890.2876.378
plotGenome11.571 0.08912.680
processAD5.6080.0256.077
readMethods4.3900.0234.699
readMeths4.5550.1885.213
segData-class5.5420.0826.656
segmentSeq-package5.5870.0306.162
thresholdFinder5.2950.1965.822