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This page was generated on 2024-03-04 11:36:38 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 652/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.43.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/epigenomix
git_branch: devel
git_last_commit: 6ba7351
git_last_commit_date: 2023-10-24 09:53:11 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

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: 1.43.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epigenomix_1.43.0.tar.gz
StartedAt: 2024-03-01 21:58:38 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 22:04:12 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 333.7 seconds
RetCode: 0
Status:   OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epigenomix_1.43.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/epigenomix.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.43.0’
* 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 R 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotChains    34.559  0.227  40.666
bayesMixModel 18.362  0.224  18.586
mlMixModel     7.889  0.072   7.961
* 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: OK


Installation output

epigenomix.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL epigenomix
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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-class0.0020.0000.002
MixModel-class0.0010.0000.000
MixModelBayes-class0.0010.0000.001
MixModelML-class000
MixtureComponent-class000
bayesMixModel18.362 0.22418.586
calculateCrossCorrelation0.6260.0560.683
eSet0.0080.0040.013
fpkm0.0270.0030.031
getAlignmentQuality000
integrateData0.1460.0000.147
mappedReads0.0280.0000.028
matchProbeToPromoter0.2540.0040.257
mlMixModel7.8890.0727.961
normalize0.1680.0000.169
normalizeChIP0.0960.0000.096
plotChains34.559 0.22740.666
plotClassification0.0560.0000.101
plotComponents0.0730.0000.073
summarizeReads0.5940.0120.606
transToTSS0.0010.0040.006