Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 670/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.48.1  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/epigenomix
git_branch: RELEASE_3_21
git_last_commit: 0d6f5eb
git_last_commit_date: 2025-05-08 12:27:44 -0400 (Thu, 08 May 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for epigenomix on kunpeng2

To the developers/maintainers of the epigenomix package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epigenomix.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: epigenomix
Version: 1.48.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epigenomix_1.48.1.tar.gz
StartedAt: 2025-10-14 08:53:50 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 09:00:53 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 422.6 seconds
RetCode: 0
Status:   OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epigenomix_1.48.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/epigenomix.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.48.1’
* 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 ‘epigenomix’ 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) MixModel-class.Rd:77-81: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModel-class.Rd:85-86: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModel-class.Rd:87: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModel-class.Rd:88-89: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:55: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:56-58: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:59-60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:65-66: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:67-68: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:69-70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelBayes-class.Rd:71-72: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:51-53: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:58: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:59-60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MixModelML-class.Rd:61: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:50-55: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:56-60: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:61-63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalize.Rd:64-72: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:35-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:39-46: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:47-51: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) normalizeChIP.Rd:52-53: Lost braces in \enumerate; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ChIPseqSet-class.Rd: RangedSummarizedExperiment-class
  calculateCrossCorrelation.Rd: GRanges, GRanges-class
  eSet.Rd: ExpressionSet-class
  integrateData.Rd: ExpressionSet
  mappedReads.Rd: GRangesList-class, GRanges-class
  normalize.Rd: ExpressionSet-class
  summarizeReads.Rd: countOverlaps
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
plotChains    37.861  0.189  45.899
bayesMixModel 30.167  1.368  31.655
mlMixModel    15.674  0.127  16.566
* 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/epigenomix.Rcheck/00check.log’
for details.


Installation output

epigenomix.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL epigenomix
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘epigenomix’ ...
** this is package ‘epigenomix’ version ‘1.48.1’
** 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 (epigenomix)

Tests output


Example timings

epigenomix.Rcheck/epigenomix-Ex.timings

nameusersystemelapsed
ChIPseqSet-class0.0010.0000.001
MixModel-class0.0000.0000.001
MixModelBayes-class0.0010.0000.000
MixModelML-class0.0000.0000.001
MixtureComponent-class0.0010.0000.002
bayesMixModel30.167 1.36831.655
calculateCrossCorrelation0.8980.0720.973
eSet0.0110.0030.015
fpkm0.0270.0040.033
getAlignmentQuality000
integrateData0.2190.0040.223
mappedReads0.0390.0000.040
matchProbeToPromoter0.4060.0240.432
mlMixModel15.674 0.12716.566
normalize0.2660.0000.531
normalizeChIP0.1600.0000.321
plotChains37.861 0.18945.899
plotClassification0.0370.0040.042
plotComponents0.0570.0000.060
summarizeReads0.4470.0040.456
transToTSS0.0040.0000.006