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This page was generated on 2025-01-16 12:11 -0500 (Thu, 16 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4489
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4387
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 865/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.2.0  (landing page)
Angelo Velle
Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 2025)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: RELEASE_3_20
git_last_commit: eb9ddba
git_last_commit_date: 2024-10-29 11:30:48 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for gINTomics on taishan

To the developers/maintainers of the gINTomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.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: gINTomics
Version: 1.2.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics
StartedAt: 2025-01-14 12:58:30 -0000 (Tue, 14 Jan 2025)
EndedAt: 2025-01-14 13:09:58 -0000 (Tue, 14 Jan 2025)
EllapsedTime: 687.1 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 gINTomics
###
##############################################################################
##############################################################################


* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* preparing ‘gINTomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gINTomics.Rmd’ using rmarkdown
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:08] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:08] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-01-14 13:00:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-01-14 13:00:37] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-14 13:00:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 13:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:37] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-14 13:00:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 13:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-14 13:00:37] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-14 13:00:37] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-14 13:00:37] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-14 13:00:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-14 13:03:42] [WARN]    [OmnipathR] HTTP 404
[2025-01-14 13:03:42] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2025-01-14 13:03:47] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-14 13:06:49] [WARN]    [OmnipathR] HTTP 404
[2025-01-14 13:06:49] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2025-01-14 13:06:54] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-14 13:09:56] [WARN]    [OmnipathR] HTTP 404
[2025-01-14 13:09:56] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404

Quitting from lines 139-142 [unnamed-chunk-9] (gINTomics.Rmd)
Error: processing vignette 'gINTomics.Rmd' failed with diagnostics:
ℹ In index: 1.
ℹ With name: hsa.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 404
--- failed re-building ‘gINTomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted