Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-15 11:05:55 -0500 (Sat, 15 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4160
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
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? here 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 580/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.25.1  (landing page)
Ludwig Geistlinger
Snapshot Date: 2022-01-14 13:55:18 -0500 (Fri, 14 Jan 2022)
git_url: https://git.bioconductor.org/packages/EnrichmentBrowser
git_branch: master
git_last_commit: f794051
git_last_commit_date: 2021-12-15 18:43:35 -0500 (Wed, 15 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
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  UNNEEDED, same version is already published

Summary

Package: EnrichmentBrowser
Version: 2.25.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings EnrichmentBrowser_2.25.1.tar.gz
StartedAt: 2022-01-14 19:05:40 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 19:10:39 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 299.4 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichmentBrowser.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings EnrichmentBrowser_2.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/EnrichmentBrowser.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘2.25.1’
* 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    74.506  2.860  77.373
getGenesets 12.789  0.476  19.630
eaBrowse     7.388  0.511   7.909
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.



Installation output

EnrichmentBrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL EnrichmentBrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
combResults1.1940.0031.199
compileGRN3.3780.0913.469
configEBrowser0.0000.0010.001
deAna3.3150.1953.510
downloadPathways000
eaBrowse7.3880.5117.909
ebrowser74.506 2.86077.373
getGenesets12.789 0.47619.630
ggeaGraph4.0400.1004.139
idMap0.6510.0960.747
import3.8210.0723.892
isAvailable0.0000.0000.001
makeExampleData0.0220.0030.025
nbea0.2390.0120.250
normalize0.3960.0240.421
plots1.2640.0641.328
probe2gene0.0630.0000.063
readSE0.0320.0000.032
sbea0.1630.0000.163