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CHECK report for EnrichmentBrowser on malbec2

This page was generated on 2020-10-17 11:54:43 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE EnrichmentBrowser PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 545/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.18.2
Ludwig Geistlinger
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/EnrichmentBrowser
Branch: RELEASE_3_11
Last Commit: 1950f79
Last Changed Date: 2020-09-15 15:53:21 -0400 (Tue, 15 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EnrichmentBrowser
Version: 2.18.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings EnrichmentBrowser_2.18.2.tar.gz
StartedAt: 2020-10-17 01:03:39 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:09:05 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 326.0 seconds
RetCode: 0
Status:  OK 
CheckDir: EnrichmentBrowser.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings EnrichmentBrowser_2.18.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.18.2’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
ebrowser    71.464  1.092  75.273
getGenesets 16.651  0.100  20.657
eaBrowse    11.652  0.321  16.294
* 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-3.11-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.



Installation output

EnrichmentBrowser.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL EnrichmentBrowser
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘EnrichmentBrowser’ ...
** using staged installation
** 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 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 (EnrichmentBrowser)

Tests output


Example timings

EnrichmentBrowser.Rcheck/EnrichmentBrowser-Ex.timings

nameusersystemelapsed
combResults0.9830.0241.008
compileGRN3.8720.0643.972
configEBrowser0.0000.0000.001
deAna4.8220.1444.994
downloadPathways000
eaBrowse11.652 0.32116.294
ebrowser71.464 1.09275.273
getGenesets16.651 0.10020.657
ggeaGraph3.2490.0163.265
idMap0.5550.0440.620
isAvailable000
makeExampleData0.0290.0000.028
nbea0.2820.0040.286
normalize0.7450.0040.764
plots1.2110.0161.228
probe2gene0.1340.0040.138
readSE0.0880.0000.088
sbea0.3290.0080.345