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CHECK report for epihet on celaya2

This page was generated on 2019-10-16 13:03:57 -0400 (Wed, 16 Oct 2019).

Package 509/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epihet 1.0.0
Xiaowen Chen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/epihet
Branch: RELEASE_3_9
Last Commit: 19d2d7d
Last Changed Date: 2019-05-02 11:54:14 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: epihet
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epihet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epihet_1.0.0.tar.gz
StartedAt: 2019-10-16 02:36:39 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:41:50 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 311.3 seconds
RetCode: 0
Status:  OK 
CheckDir: epihet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epihet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epihet_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/epihet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epihet/DESCRIPTION’ ... OK
* this is package ‘epihet’ version ‘1.0.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
epiPathway 22.599  3.066  25.669
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/epihet.Rcheck/00check.log’
for details.



Installation output

epihet.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL epihet
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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
compMatrix1.1920.0841.275
epiBox0.0880.0090.097
epiMA0.0130.0040.018
epiMap0.1960.0210.217
epiPCA0.6820.0490.743
epiPathway22.599 3.06625.669
epiTSNE0.5070.0270.534
jaccard0.0130.0100.022
makeGR0.2240.0600.289
moduleAnno0.5430.0920.636
moduleSim0.1840.0350.221
moduleVisual0.2080.0050.214
readGR0.0400.0140.055
shannon0.0000.0000.001
splitn0.0000.0010.001
summarize0.1390.0010.141
userobj0.0210.0000.022