Multiple platform build/check report for BioC 3.22 - CHECK results for epigenomix on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4816
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4605
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4549
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4560
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*

CHECK results for epigenomix on lconway

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.

raw results

Summary

Package: epigenomix

Version: 1.49.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings epigenomix_1.49.0.tar.gz

StartedAt: 2025-09-22 20:51:28 -0400 (Mon, 22 Sep 2025)

EndedAt: 2025-09-22 20:56:46 -0400 (Mon, 22 Sep 2025)

EllapsedTime: 318.2 seconds

RetCode: 0

Status: OK

CheckDir: epigenomix.Rcheck

Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings epigenomix_1.49.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/epigenomix.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.49.0’
* 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 ‘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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotChains    24.173  0.317  24.589
bayesMixModel 21.215  0.245  21.594
mlMixModel    10.081  0.173  10.349
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/epigenomix.Rcheck/00check.log’
for details.

Installation output

epigenomix.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL epigenomix
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘epigenomix’ ...
** this is package ‘epigenomix’ version ‘1.49.0’
** 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 (epigenomix)

Tests output

Example timings

epigenomix.Rcheck/epigenomix-Ex.timings

name	user	system	elapsed
ChIPseqSet-class	0.001	0.000	0.002
MixModel-class	0.001	0.000	0.001
MixModelBayes-class	0.000	0.000	0.001
MixModelML-class	0.000	0.001	0.000
MixtureComponent-class	0	0	0
bayesMixModel	21.215	0.245	21.594
calculateCrossCorrelation	0.807	0.010	0.822
eSet	0.012	0.002	0.015
fpkm	0.030	0.004	0.035
getAlignmentQuality	0	0	0
integrateData	0.180	0.001	0.182
mappedReads	0.034	0.002	0.037
matchProbeToPromoter	0.349	0.003	0.357
mlMixModel	10.081	0.173	10.349
normalize	0.159	0.001	0.161
normalizeChIP	0.119	0.002	0.122
plotChains	24.173	0.317	24.589
plotClassification	0.028	0.002	0.029
plotComponents	0.036	0.002	0.038
summarizeReads	0.308	0.001	0.309
transToTSS	0.002	0.001	0.004