Back to Multiple platform build/check report for BioC 3.13
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-07-23 15:05:38 -0400 (Fri, 23 Jul 2021).

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 573/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.22.2  (landing page)
Ludwig Geistlinger
Snapshot Date: 2021-07-22 04:50:13 -0400 (Thu, 22 Jul 2021)
URL: https://git.bioconductor.org/packages/EnrichmentBrowser
Branch: RELEASE_3_13
Last Commit: e3ba414
Last Changed Date: 2021-07-21 08:44:59 -0400 (Wed, 21 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: EnrichmentBrowser
Version: 2.22.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings EnrichmentBrowser_2.22.2.tar.gz
StartedAt: 2021-07-22 09:41:54 -0400 (Thu, 22 Jul 2021)
EndedAt: 2021-07-22 09:47:02 -0400 (Thu, 22 Jul 2021)
EllapsedTime: 308.1 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichmentBrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings EnrichmentBrowser_2.22.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘2.22.2’
* 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
.exportToEnrichplot: no visible binding for global variable ‘se’
.getGOFromBiomart: no visible binding for global variable
  ‘go_linkage_type’
.res2result: no visible binding for global variable ‘se’
Undefined global functions or variables:
  go_linkage_type se
* 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    71.173  1.408  72.589
getGenesets 13.626  0.452  19.466
eaBrowse     9.368  0.312   9.689
compileGRN   5.632  0.720   6.351
deAna        5.424  0.315   5.741
import       5.569  0.124   5.693
* 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-3.13-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.



Installation output

EnrichmentBrowser.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL EnrichmentBrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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
combResults0.5740.0200.594
compileGRN5.6320.7206.351
configEBrowser0.0010.0000.001
deAna5.4240.3155.741
downloadPathways000
eaBrowse9.3680.3129.689
ebrowser71.173 1.40872.589
getGenesets13.626 0.45219.466
ggeaGraph3.7140.0713.786
idMap0.7290.0920.821
import5.5690.1245.693
isAvailable000
makeExampleData0.0380.0000.038
nbea0.2950.0000.294
normalize0.6010.0280.630
plots1.1180.0721.191
probe2gene0.0850.0040.089
readSE0.0510.0000.052
sbea0.3850.0000.386