Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:06 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 EnrichmentBrowser on lconway


To the developers/maintainers of the EnrichmentBrowser package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnrichmentBrowser.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 610/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.28.2  (landing page)
Ludwig Geistlinger
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/EnrichmentBrowser
git_branch: RELEASE_3_16
git_last_commit: 0db911d
git_last_commit_date: 2023-03-19 19:26:11 -0400 (Sun, 19 Mar 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EnrichmentBrowser
Version: 2.28.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnrichmentBrowser_2.28.2.tar.gz
StartedAt: 2023-04-10 20:03:30 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:09:12 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 341.4 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichmentBrowser.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnrichmentBrowser_2.28.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.28.2’
* 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 ... NOTE
.getGOFromBiomart: no visible binding for global variable
  ‘go_linkage_type’
Undefined global functions or variables:
  go_linkage_type
* 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 (user + system) or elapsed time > 5s
              user system elapsed
ebrowser    74.291 34.764 110.128
getGenesets 13.167  0.690  22.555
eaBrowse     7.934  0.935   8.922
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.



Installation output

EnrichmentBrowser.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EnrichmentBrowser
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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
combResults0.4570.0290.487
compileGRN4.2540.2844.546
configEBrowser000
deAna3.2470.1243.379
downloadPathways000
eaBrowse7.9340.9358.922
ebrowser 74.291 34.764110.128
getGenesets13.167 0.69022.555
ggeaGraph3.4090.1493.562
idMap0.6430.0860.730
import3.3350.0783.418
isAvailable0.0000.0000.001
makeExampleData0.0280.0000.028
nbea0.3770.0740.469
normalize0.3610.0360.398
plots1.0900.0941.191
probe2gene0.1930.0390.233
readSE0.0330.0010.034
sbea0.1560.0030.159