Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 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 512/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decoupleR 2.11.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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. |
Package: decoupleR |
Version: 2.11.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR |
StartedAt: 2024-06-09 18:22:47 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 18:27:25 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 278.2 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### 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 2024-06-09 18:23:17.413 R[45879:460587516] XType: com.apple.fonts is not accessible. 2024-06-09 18:23:17.415 R[45879:460587516] XType: XTFontStaticRegistry is enabled. --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2024-06-09 18:23:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:23:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:44] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-06-09 18:23:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-09 18:23:44] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-06-09 18:23:44] [TRACE] [OmnipathR] Contains 1 files. [2024-06-09 18:23:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-09 18:23:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:23:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-06-09 18:23:44] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-09 18:23:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-09 18:23:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-09 18:23:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-09 18:23:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-09 18:23:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:44] [TRACE] [OmnipathR] Cache locked: FALSE [2024-06-09 18:23:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-06-09 18:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:45] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:23:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:45] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:23:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:23:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:45] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-06-09 18:23:45] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-06-09 18:23:45] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:23:45] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:23:46] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:23:46] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:23:51] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:23:51] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:23:51] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:23:56] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:23:56] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:23:56] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:23:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:23:56] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:23:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:23:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:23:56] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2024-06-09 18:23:57] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2024-06-09 18:23:57] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:23:57] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:23:57] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:23:57] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:24:02] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:24:02] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:24:02] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:24:07] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:24:07] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:24:07] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:24:07] [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. [2024-06-09 18:24:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:24:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:24:08] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:24:08] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:24:08] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:24:12] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:24:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:24:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:24:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:24:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:24:12] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2024-06-09 18:24:12] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-06-09 18:24:17] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-06-09 18:24:17] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2024-06-09 18:24:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:24:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:24:17] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2024-06-09 18:24:17] [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 [2024-06-09 18:25:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-06-09 18:25:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:25:04] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:25:04] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:25:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:25:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:25:04] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3. [2024-06-09 18:25:04] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html [2024-06-09 18:25:04] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:04] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:04] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:04] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:25:09] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:09] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:09] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:25:14] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:15] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:15] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:25:15] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:25:15] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:25:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:25:15] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4. [2024-06-09 18:25:15] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html [2024-06-09 18:25:15] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:15] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:15] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:15] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:25:20] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:20] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:20] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:25:25] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:26] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:26] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:25:26] [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. [2024-06-09 18:25:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:25:29] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-06-09 18:25:29] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-06-09 18:25:29] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2024-06-09 18:25:44] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:25:44] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:25:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:25:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:25:44] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5. [2024-06-09 18:25:44] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html [2024-06-09 18:25:44] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:44] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:45] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:45] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:25:50] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:50] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:50] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:25:55] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:55] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:55] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:25:55] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:25:55] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:25:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:25:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:25:55] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6. [2024-06-09 18:25:55] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html [2024-06-09 18:25:55] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:55] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:25:55] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:25:55] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:26:00] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:01] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:26:01] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:26:06] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:06] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:26:06] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:26:06] [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. [2024-06-09 18:26:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:26:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:26:06] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:26:06] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:26:06] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:26:09] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:26:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:26:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:26:09] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`. [2024-06-09 18:26:09] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-06-09 18:26:10] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-06-09 18:26:10] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2024-06-09 18:26:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:26:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:26:10] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`. [2024-06-09 18:26:10] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-06-09 18:26:22] [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 [2024-06-09 18:26:38] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:26:38] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:26:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:26:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:26:38] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7. [2024-06-09 18:26:38] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html [2024-06-09 18:26:38] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:38] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:39] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:26:39] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:26:44] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:44] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:26:44] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:26:49] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:49] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:26:49] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:26:49] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-06-09 18:26:49] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-06-09 18:26:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-09 18:26:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-09 18:26:49] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8. [2024-06-09 18:26:49] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html [2024-06-09 18:26:49] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:50] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:50] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:26:50] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-06-09 18:26:55] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:26:55] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:26:55] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-06-09 18:27:00] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-06-09 18:27:00] [WARN] [OmnipathR] HTTP 403 [2024-06-09 18:27:00] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 [2024-06-09 18:27:00] [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. [2024-06-09 18:27:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:27:01] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-06-09 18:27:01] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-06-09 18:27:01] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-06-09 18:27:12] [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