Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:05:44 -0400 (Fri, 24 Sep 2021).

CHECK results for epihet on nebbiolo1

To the developers/maintainers of the epihet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epihet.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 584/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epihet 1.8.0  (landing page)
Xiaowen Chen
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/epihet
git_branch: RELEASE_3_13
git_last_commit: cffe2bb
git_last_commit_date: 2021-05-19 12:39:58 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: epihet
Version: 1.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:epihet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings epihet_1.8.0.tar.gz
StartedAt: 2021-09-23 09:43:06 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 09:45:57 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 171.2 seconds
RetCode: 0
Status:   OK  
CheckDir: epihet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:epihet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings epihet_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/epihet.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epihet/DESCRIPTION’ ... OK
* this is package ‘epihet’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GenomicRanges', 'IRanges', 'S4Vectors', 'ggplot2', 'foreach',
  'Rtsne', 'igraph'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘epihet’ 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
epiPathway 11.719  0.208  11.928
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/epihet.Rcheck/00check.log’
for details.



Installation output

epihet.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL epihet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘epihet’ ...
** 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 (epihet)

Tests output


Example timings

epihet.Rcheck/epihet-Ex.timings

nameusersystemelapsed
compMatrix0.4050.0010.404
epiBox0.0310.0000.030
epiMA0.0060.0000.006
epiMap0.0650.0030.069
epiPCA0.2700.0120.282
epiPathway11.719 0.20811.928
epiTSNE0.1350.0000.135
jaccard0.0060.0000.006
makeGR0.1170.0090.125
moduleAnno0.1580.0070.165
moduleSim0.0260.0050.030
moduleVisual0.0830.0200.102
readGR0.0190.0100.028
shannon0.0000.0000.001
splitn0.0000.0000.001
summarize0.1300.0070.137
userobj0.0270.0040.030