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This page was generated on 2022-11-26 11:05:24 -0500 (Sat, 26 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4201
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
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 nebbiolo1


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 600/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.29.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-11-25 14:00:12 -0500 (Fri, 25 Nov 2022)
git_url: https://git.bioconductor.org/packages/EnrichmentBrowser
git_branch: master
git_last_commit: ce09298
git_last_commit_date: 2022-11-01 11:10:18 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SummarizedExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'edgeR' which is not available

Summary

Package: EnrichmentBrowser
Version: 2.29.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EnrichmentBrowser_2.29.0.tar.gz
StartedAt: 2022-11-25 20:16:24 -0500 (Fri, 25 Nov 2022)
EndedAt: 2022-11-25 20:23:15 -0500 (Fri, 25 Nov 2022)
EllapsedTime: 411.2 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichmentBrowser.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EnrichmentBrowser_2.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EnrichmentBrowser.Rcheck’
* using R Under development (unstable) (2022-10-25 r83175)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.29.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
ebrowser    75.290  2.292  77.586
getGenesets 12.795  0.524  20.079
eaBrowse     8.632  0.644   9.279
ggeaGraph    4.457  0.644   5.101
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘EnrichmentBrowser.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.



Installation output

EnrichmentBrowser.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL EnrichmentBrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
combResults0.4880.0400.528
compileGRN4.6640.2294.894
configEBrowser0.0000.0000.001
deAna3.7510.1163.867
downloadPathways000
eaBrowse8.6320.6449.279
ebrowser75.290 2.29277.586
getGenesets12.795 0.52420.079
ggeaGraph4.4570.6445.101
idMap0.6860.1040.790
import3.8140.1874.001
isAvailable000
makeExampleData0.0290.0000.028
nbea0.4300.0240.454
normalize0.4050.0400.445
plots1.2130.1401.354
probe2gene0.0700.0000.071
readSE0.0340.0040.037
sbea0.1820.0160.199