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This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
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 100/425HostnameOS / ArchINSTALLBUILDCHECK
dorothea 1.17.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2024-07-02 07:30 -0400 (Tue, 02 Jul 2024)
git_url: https://git.bioconductor.org/packages/dorothea
git_branch: devel
git_last_commit: 82df493
git_last_commit_date: 2024-04-30 11:07:06 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped


BUILD results for dorothea on nebbiolo2

To the developers/maintainers of the dorothea 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: dorothea
Version: 1.17.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dorothea
StartedAt: 2024-07-02 10:22:17 -0400 (Tue, 02 Jul 2024)
EndedAt: 2024-07-02 10:33:11 -0400 (Tue, 02 Jul 2024)
EllapsedTime: 654.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dorothea
###
##############################################################################
##############################################################################


* checking for file ‘dorothea/DESCRIPTION’ ... OK
* preparing ‘dorothea’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dorothea.Rmd’ using rmarkdown
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Contains 8 files.
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-02 10:23:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-07-02 10:23:02] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:02] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:23:02] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-07-02 10:23:02] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:23:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:24:33] [WARN]    [OmnipathR] HTTP 504
[2024-07-02 10:24:33] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504
[2024-07-02 10:24:38] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:26:08] [WARN]    [OmnipathR] HTTP 504
[2024-07-02 10:26:08] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504
[2024-07-02 10:26:13] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:27:44] [WARN]    [OmnipathR] HTTP 504
[2024-07-02 10:27:44] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504
[2024-07-02 10:27:44] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-07-02 10:27:44] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-07-02 10:27:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:27:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:27:44] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-07-02 10:27:44] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-07-02 10:27:44] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:27:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:29:14] [WARN]    [OmnipathR] HTTP 504
[2024-07-02 10:29:14] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504
[2024-07-02 10:29:19] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:30:50] [WARN]    [OmnipathR] HTTP 504
[2024-07-02 10:30:50] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504
[2024-07-02 10:30:55] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-07-02 10:32:26] [WARN]    [OmnipathR] HTTP 504
[2024-07-02 10:32:26] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504
[2024-07-02 10:32:26] [WARN]    [OmnipathR] Accessing `dorothea` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2024-07-02 10:32:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-07-02 10:32:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-07-02 10:32:26] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-07-02 10:32:26] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-07-02 10:32:27] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-07-02 10:32:34] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-07-02 10:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:32:34] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`.
[2024-07-02 10:32:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-07-02 10:32:36] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-07-02 10:32:36] [INFO]    [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1]
[2024-07-02 10:32:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-02 10:32:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-02 10:32:36] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`.
[2024-07-02 10:32:36] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-07-02 10:32:52] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any

Quitting from lines 67-69 [model] (dorothea.Rmd)
Error: processing vignette 'dorothea.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘dorothea.Rmd’

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

Error: Vignette re-building failed.
Execution halted