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This page was generated on 2022-08-12 11:06:38 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4167
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

BUILD results for pathview on palomino4


To the developers/maintainers of the pathview package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathview.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 1418/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathview 1.37.0  (landing page)
Weijun Luo
Snapshot Date: 2022-08-11 14:00:04 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/pathview
git_branch: master
git_last_commit: 272618d
git_last_commit_date: 2022-04-26 11:13:56 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: pathview
Version: 1.37.0
Command: chmod a+r pathview -R && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pathview
StartedAt: 2022-08-11 20:22:03 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 20:22:32 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 28.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r pathview -R && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data pathview
###
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* checking for file 'pathview/DESCRIPTION' ... OK
* preparing 'pathview':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'pathview.Rnw' using Sweave

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
Info: Downloading xml files for hsa04110, 1/1 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
  URL 'https://rest.kegg.jp/get/hsa04110/kgml': status was 'Failure when receiving data from the peer'
Warning: Download of hsa04110 xml file failed!
This pathway may not exist!
Info: Downloading png files for hsa04110, 1/1 pathways..
Warning: Download of hsa04110 png file failed!
This pathway may not exist!
Warning: Failed to download KEGG xml/png files, hsa04110 skipped!

Error: processing vignette 'pathview.Rnw' failed with diagnostics:
 chunk 15 (label = kegg.native) 
Error in pv.out$plot.data.gene : $ operator is invalid for atomic vectors

--- failed re-building 'pathview.Rnw'

SUMMARY: processing the following file failed:
  'pathview.Rnw'

Error: Vignette re-building failed.
Execution halted