Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1534/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pgxRpi 1.2.0  (landing page)
Hangjia Zhao
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/pgxRpi
git_branch: RELEASE_3_20
git_last_commit: b979290
git_last_commit_date: 2024-10-29 11:25:45 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for pgxRpi on kunpeng2

To the developers/maintainers of the pgxRpi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pgxRpi.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: pgxRpi
Version: 1.2.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
StartedAt: 2024-11-20 02:55:55 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 03:08:13 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 738.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
###
##############################################################################
##############################################################################


* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* preparing ‘pgxRpi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_1_loadmetadata.Rmd’ using rmarkdown
--- finished re-building ‘Introduction_1_loadmetadata.Rmd’

--- re-building ‘Introduction_2_loadvariants.Rmd’ using rmarkdown

Quitting from lines 169-170 [unnamed-chunk-12] (Introduction_2_loadvariants.Rmd)
Error: processing vignette 'Introduction_2_loadvariants.Rmd' failed with diagnostics:
cannot open the connection to 'http://progenetix.org/services/samplematrix/?filters=NCIT:C2948&limit=0'
--- failed re-building ‘Introduction_2_loadvariants.Rmd’

--- re-building ‘Introduction_3_loadfrequency.Rmd’ using rmarkdown
--- finished re-building ‘Introduction_3_loadfrequency.Rmd’

--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_2_loadvariants.Rmd’

Error: Vignette re-building failed.
Execution halted