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This page was generated on 2024-06-07 20:26 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 527/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.10.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: RELEASE_3_19
git_last_commit: 7e6c106
git_last_commit_date: 2024-04-30 11:34:47 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for decoupleR on lconway

To the developers/maintainers of the decoupleR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.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: decoupleR
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
StartedAt: 2024-06-05 16:25:34 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 16:28:43 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 188.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
###
##############################################################################
##############################################################################


* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* preparing ‘decoupleR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘decoupleR.Rmd’ using rmarkdown
2024-06-05 16:25:51.212 R[64384:13682613] XType: com.apple.fonts is not accessible.
2024-06-05 16:25:51.217 R[64384:13682613] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:07] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:07] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:08] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:08] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:08] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-06-05 16:26:08] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:09] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:26:09] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:26:14] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:15] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:26:15] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:26:20] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:20] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:26:20] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:26:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:26:20] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:20] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-06-05 16:26:20] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-06-05 16:26:20] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:20] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:26:20] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:26:25] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:25] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:26:25] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:26:30] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:26:30] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:26:30] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:26:30] [WARN]    [OmnipathR] Accessing `PROGENy` 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.
[2024-06-05 16:26:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:26:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:26:34] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:26:34] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:26:34] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:26:42] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:26:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:42] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`.
[2024-06-05 16:26:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-05 16:26:44] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-05 16:26:44] [INFO]    [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1]
[2024-06-05 16:26:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:26:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:26:44] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`.
[2024-06-05 16:26:44] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
Warning: ggrepel: 443 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2024-06-05 16:27:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-05 16:27:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:27:05] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:27:05] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:27:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:27:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:27:05] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2024-06-05 16:27:05] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2024-06-05 16:27:05] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:05] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:05] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:27:10] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:10] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:10] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:27:15] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:16] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:16] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:27:16] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:27:16] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:27:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:27:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:27:16] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2024-06-05 16:27:16] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2024-06-05 16:27:16] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:16] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:16] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:27:21] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:21] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:21] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:27:26] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:26] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:26] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:27:26] [WARN]    [OmnipathR] Accessing `PROGENy` 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.
[2024-06-05 16:27:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:27:28] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-05 16:27:28] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-05 16:27:28] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.

  |                                                                                                                    
  |                                                                                                              |   0%
  |                                                                                                                    
  |==============================================================================================================| 100%
--- finished re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2024-06-05 16:27:37] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:27:37] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:27:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:27:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:27:37] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2024-06-05 16:27:37] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2024-06-05 16:27:37] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:37] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:37] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:27:42] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:42] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:42] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:27:47] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:47] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:47] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:27:48] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:27:48] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:27:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:27:48] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6.
[2024-06-05 16:27:48] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html
[2024-06-05 16:27:48] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:48] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:48] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:27:53] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:53] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:53] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:27:58] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:27:58] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:27:58] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:27:58] [WARN]    [OmnipathR] Accessing `collectri` 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.
[2024-06-05 16:27:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:27:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:27:58] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:27:58] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:27:58] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:28:00] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:28:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:28:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:28:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:28:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:28:00] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2024-06-05 16:28:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-05 16:28:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-05 16:28:01] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2024-06-05 16:28:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:28:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:28:01] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2024-06-05 16:28:01] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-05 16:28:06] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from lines 118-120 [collectri] (tf_bk.Rmd)
Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2024-06-05 16:28:10] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:28:10] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:28:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:28:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:28:10] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7.
[2024-06-05 16:28:10] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html
[2024-06-05 16:28:10] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:11] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:28:11] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:28:16] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:16] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:28:16] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:28:21] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:21] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:28:21] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:28:21] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-05 16:28:21] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-05 16:28:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-05 16:28:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-05 16:28:21] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8.
[2024-06-05 16:28:21] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html
[2024-06-05 16:28:21] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:21] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:28:21] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-05 16:28:26] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:26] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:28:27] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-05 16:28:32] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-05 16:28:32] [WARN]    [OmnipathR] HTTP 403
[2024-06-05 16:28:32] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-05 16:28:32] [WARN]    [OmnipathR] Accessing `collectri` 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.
[2024-06-05 16:28:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:28:32] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-05 16:28:32] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-05 16:28:32] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-05 16:28:37] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from lines 86-88 [collectri] (tf_sc.Rmd)
Error: processing vignette 'tf_sc.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘tf_sc.Rmd’

SUMMARY: processing the following files failed:
  ‘tf_bk.Rmd’ ‘tf_sc.Rmd’

Error: Vignette re-building failed.
Execution halted