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CHECK report for EnrichmentBrowser on merida2

This page was generated on 2018-10-17 08:53:34 -0400 (Wed, 17 Oct 2018).

Package 447/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.10.11
Ludwig Geistlinger
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/EnrichmentBrowser
Branch: RELEASE_3_7
Last Commit: 96bfeea
Last Changed Date: 2018-08-26 17:23:02 -0400 (Sun, 26 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: EnrichmentBrowser
Version: 2.10.11
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnrichmentBrowser_2.10.11.tar.gz
StartedAt: 2018-10-16 21:11:33 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:17:25 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 351.3 seconds
RetCode: 0
Status:  OK 
CheckDir: EnrichmentBrowser.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EnrichmentBrowser_2.10.11.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.10.11’
* package encoding: UTF-8
* 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 ‘EnrichmentBrowser’ 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 ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
  See the note in ?`:::` about the use of this operator.
* 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 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
ebrowser    82.025 23.547 107.296
getGenesets 17.653  0.227  21.779
compileGRN  11.621  1.852  13.588
eaBrowse     9.919  0.869  11.461
* 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-3.7-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.



Installation output

EnrichmentBrowser.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EnrichmentBrowser
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘EnrichmentBrowser’ ...
** R
** 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
* DONE (EnrichmentBrowser)

Tests output


Example timings

EnrichmentBrowser.Rcheck/EnrichmentBrowser-Ex.timings

nameusersystemelapsed
combResults0.5690.0440.616
compileGRN11.621 1.85213.588
configEBrowser0.0010.0000.002
deAna3.2820.1573.477
downloadPathways0.0010.0000.001
eaBrowse 9.919 0.86911.461
ebrowser 82.025 23.547107.296
getGenesets17.653 0.22721.779
ggeaGraph0.9930.0241.028
idMap0.3300.0240.358
isAvailable0.0020.0000.001
makeExampleData0.0310.0000.031
nbea0.4180.0050.429
normalize1.8190.0521.900
plots0.9820.0061.009
probe2gene0.0830.0050.089
readSE0.0620.0050.067
sbea0.2190.0020.225