Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-27 11:05:39 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 589/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.35.1  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/epigenomix
git_branch: master
git_last_commit: bf5904f
git_last_commit_date: 2021-11-18 19:30:22 -0500 (Thu, 18 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epigenomix
Version: 1.35.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings epigenomix_1.35.1.tar.gz
StartedAt: 2022-01-26 19:10:28 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 19:14:17 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 229.2 seconds
RetCode: 0
Status:   OK  
CheckDir: epigenomix.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings epigenomix_1.35.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/epigenomix.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epigenomix/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epigenomix’ version ‘1.35.1’
* 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 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 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    22.009  0.232  22.242
bayesMixModel 17.015  0.368  17.382
mlMixModel     7.801  0.156   7.957
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

epigenomix.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL epigenomix
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-class0.0010.0000.002
MixModel-class0.0010.0000.001
MixModelBayes-class0.0010.0000.001
MixModelML-class0.0010.0000.001
MixtureComponent-class000
bayesMixModel17.015 0.36817.382
calculateCrossCorrelation0.5900.0160.607
eSet0.0080.0040.012
fpkm0.030.000.03
getAlignmentQuality000
integrateData0.1400.0120.152
mappedReads0.0250.0040.029
matchProbeToPromoter0.2540.0080.262
mlMixModel7.8010.1567.957
normalize0.1540.0160.170
normalizeChIP0.1140.0040.118
plotChains22.009 0.23222.242
plotClassification0.0260.0000.026
plotComponents0.0310.0040.036
summarizeReads0.2580.0040.262
transToTSS0.0030.0000.003