Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 661/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.44.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/epigenomix
git_branch: RELEASE_3_19
git_last_commit: cf0c49a
git_last_commit_date: 2024-04-30 10:30:52 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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


CHECK results for epigenomix on merida1

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: 1.44.0
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_1.44.0.tar.gz
StartedAt: 2024-10-17 04:51:49 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 05:03:56 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 726.8 seconds
RetCode: 0
Status:   OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

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### Running 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_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/epigenomix.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.44.0’
* 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 ... 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 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    57.724  0.681  72.367
bayesMixModel 45.630  0.786  57.661
mlMixModel    24.320  0.417  30.679
* 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-3.19-bioc/meat/epigenomix.Rcheck/00check.log’
for details.


Installation output

epigenomix.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL epigenomix
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘epigenomix’ ...
** 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-class0.0040.0010.006
MixModel-class0.0010.0010.002
MixModelBayes-class0.0000.0000.001
MixModelML-class0.0010.0010.001
MixtureComponent-class0.0010.0010.002
bayesMixModel45.630 0.78657.661
calculateCrossCorrelation1.6470.0212.037
eSet0.0220.0050.032
fpkm0.0540.0070.077
getAlignmentQuality0.0000.0000.001
integrateData0.3940.0120.486
mappedReads0.0670.0090.104
matchProbeToPromoter0.7480.0531.030
mlMixModel24.320 0.41730.679
normalize0.4430.0050.546
normalizeChIP0.2610.0050.334
plotChains57.724 0.68172.367
plotClassification0.0640.0060.089
plotComponents0.0920.0050.124
summarizeReads0.7290.0070.912
transToTSS0.0050.0050.011