Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-27 12:05:17 -0400 (Fri, 27 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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? 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 609/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epigenomix 1.36.0  (landing page)
Hans-Ulrich Klein
Snapshot Date: 2022-05-26 13:55:15 -0400 (Thu, 26 May 2022)
git_url: https://git.bioconductor.org/packages/epigenomix
git_branch: RELEASE_3_15
git_last_commit: ce6e102
git_last_commit_date: 2022-04-26 11:13:53 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epigenomix
Version: 1.36.0
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_1.36.0.tar.gz
StartedAt: 2022-05-26 19:29:30 -0400 (Thu, 26 May 2022)
EndedAt: 2022-05-26 19:33:35 -0400 (Thu, 26 May 2022)
EllapsedTime: 244.8 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_1.36.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/epigenomix.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.36.0’
* 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 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    22.367  0.192  22.561
bayesMixModel 18.036  0.343  18.380
mlMixModel     7.982  0.169   8.152
* 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
###
##############################################################################
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* 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-class0.0020.0000.002
MixModel-class0.0010.0000.001
MixModelBayes-class0.0010.0000.001
MixModelML-class000
MixtureComponent-class000
bayesMixModel18.036 0.34318.380
calculateCrossCorrelation0.6880.0810.768
eSet0.0130.0000.013
fpkm0.0270.0040.031
getAlignmentQuality000
integrateData0.1620.0040.166
mappedReads0.0310.0000.031
matchProbeToPromoter0.2720.0160.288
mlMixModel7.9820.1698.152
normalize0.1540.0060.159
normalizeChIP0.0960.0000.096
plotChains22.367 0.19222.561
plotClassification0.0280.0000.027
plotComponents0.0410.0000.041
summarizeReads0.2890.0030.294
transToTSS0.0030.0010.003