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This page was generated on 2024-05-07 11:32:33 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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Package 651/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.34.1  (landing page)
Ludwig Geistlinger
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/EnrichmentBrowser
git_branch: RELEASE_3_19
git_last_commit: 6cfc989
git_last_commit_date: 2024-05-05 18:27:16 -0400 (Sun, 05 May 2024)
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES

CHECK results for EnrichmentBrowser on kjohnson3


To the developers/maintainers of the EnrichmentBrowser package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: EnrichmentBrowser
Version: 2.34.1
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_2.34.1.tar.gz
StartedAt: 2024-05-06 21:18:52 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 21:21:23 -0400 (Mon, 06 May 2024)
EllapsedTime: 151.6 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_2.34.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/EnrichmentBrowser.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.34.1’
* 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 code 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 whether startup messages can be suppressed ... 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    31.284  8.469  39.805
getGenesets  4.724  0.181  10.154
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc-mac-arm64/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/4.4-arm64/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
combResults0.1640.0080.172
compileGRN1.7560.0581.815
configEBrowser000
deAna1.0600.0651.124
downloadPathways000
eaBrowse3.6140.2953.918
ebrowser31.284 8.46939.805
getGenesets 4.724 0.18110.154
ggeaGraph1.6450.0291.674
idMap0.2980.0630.361
import1.3100.0601.371
isAvailable000
makeExampleData0.0070.0000.008
nbea0.1250.0070.132
normalize0.1230.0220.144
plots0.4810.0440.525
probe2gene0.0180.0010.018
readSE0.0090.0010.009
sbea0.0490.0010.050