Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 848/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.1.0  (landing page)
Angelo Velle
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: devel
git_last_commit: c1c358f
git_last_commit_date: 2024-04-30 11:56:24 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for gINTomics on palomino4

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.

raw results


Summary

Package: gINTomics
Version: 1.1.0
Command: chmod a+r gINTomics -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data gINTomics
StartedAt: 2024-06-09 19:19:57 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 19:23:04 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 187.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r gINTomics -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe 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
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:23] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:23] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-09 19:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:24] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-09 19:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:24] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-09 19:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:24] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-06-09 19:22:52] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 19:22:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 19:22:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:52] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 19:22:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 19:22:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 19:22:52] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-06-09 19:22:52] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-06-09 19:22:52] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 19:22:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 19:22:53] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 19:22:53] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 19:22:58] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 19:22:58] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 19:22:58] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 19:23:03] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 19:23:03] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 19:23:03] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403

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 403
--- failed re-building 'gINTomics.Rmd'

SUMMARY: processing the following file failed:
  'gINTomics.Rmd'

Error: Vignette re-building failed.
Execution halted