Multiple platform build/check report for BioC 3.21 - CHECK results for epigenomix on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4658
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4455
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4464
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4418
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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 nebbiolo1

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: 1.47.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings epigenomix_1.47.0.tar.gz

StartedAt: 2025-01-26 22:35:53 -0500 (Sun, 26 Jan 2025)

EndedAt: 2025-01-26 22:41:47 -0500 (Sun, 26 Jan 2025)

EllapsedTime: 354.5 seconds

RetCode: 0

Status: OK

CheckDir: epigenomix.Rcheck

Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings epigenomix_1.47.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/epigenomix.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.47.0’
* 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 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
bayesMixModel 30.796  0.602  37.490
plotChains    22.372  0.203  22.577
mlMixModel     9.571  0.118   9.690
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* 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/bbs-3.21-bioc/R/bin/R CMD INSTALL epigenomix
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘epigenomix’ ...
** this is package ‘epigenomix’ version ‘1.47.0’
** 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	0.002	0.000	0.002
MixModel-class	0.000	0.000	0.001
MixModelBayes-class	0	0	0
MixModelML-class	0	0	0
MixtureComponent-class	0	0	0
bayesMixModel	30.796	0.602	37.490
calculateCrossCorrelation	1.059	0.013	1.073
eSet	0.018	0.001	0.019
fpkm	0.045	0.003	0.048
getAlignmentQuality	0.000	0.001	0.001
integrateData	0.270	0.015	0.286
mappedReads	0.049	0.001	0.050
matchProbeToPromoter	0.481	0.037	0.517
mlMixModel	9.571	0.118	9.690
normalize	0.154	0.005	0.160
normalizeChIP	0.094	0.006	0.101
plotChains	22.372	0.203	22.577
plotClassification	0.024	0.001	0.025
plotComponents	0.033	0.002	0.035
summarizeReads	0.270	0.002	0.272
transToTSS	0.003	0.000	0.003