Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-27 12:24 -0400 (Fri, 27 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4451 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
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 519/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decoupleR 2.11.0 (landing page) Pau Badia-i-Mompel
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | 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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR |
StartedAt: 2024-09-26 18:10:34 -0400 (Thu, 26 Sep 2024) |
EndedAt: 2024-09-26 18:11:51 -0400 (Thu, 26 Sep 2024) |
EllapsedTime: 77.4 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/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 --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2024-09-26 18:10:55] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:55] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-09-26 18:10:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-09-26 18:10:55] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-09-26 18:10:55] [TRACE] [OmnipathR] Contains 1 files. [2024-09-26 18:10:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-09-26 18:10:55] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-09-26 18:10:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-09-26 18:10:55] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-09-26 18:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:55] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-09-26 18:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:55] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-09-26 18:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:55] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-09-26 18:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:55] [TRACE] [OmnipathR] Cache locked: FALSE [2024-09-26 18:10:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-26 18:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:10:56] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:56] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-09-26 18:10:56] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:56] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-09-26 18:10:56] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:10:56] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-09-26 18:10:56] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-09-26 18:10:57] [TRACE] [OmnipathR] HTTP 200 [2024-09-26 18:10:57] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-09-26 18:10:57] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:57] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-09-26 18:10:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:10:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-09-26 18:10:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:10:57] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:57] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-09-26 18:10:57] [TRACE] [OmnipathR] Exporting object to RDS: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:10:57] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-09-26 18:10:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-09-26 18:10:58] [TRACE] [OmnipathR] Exported RDS to `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:10:58] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-09-26 18:10:58] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:10:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:10:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-09-26 18:10:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2024-09-26 18:10:58] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:10:58] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-26 18:10:58] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:10:58] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:10:58] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:10:58] [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. [2024-09-26 18:10:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:10:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:10:58] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:10:58] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:10:58] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:11:01] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:11:01] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:11:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:11:01] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:11:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:11:01] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2024-09-26 18:11:01] [TRACE] [OmnipathR] Exporting object to RDS: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-09-26 18:11:03] [TRACE] [OmnipathR] Exported RDS to `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-09-26 18:11:03] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2024-09-26 18:11:03] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:11:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:11:03] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2024-09-26 18:11:03] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. Warning: ggrepel: 445 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘pw_bk.Rmd’ --- re-building ‘pw_sc.Rmd’ using rmarkdown [2024-09-26 18:11:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-26 18:11:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:11:17] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:11:17] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-26 18:11:17] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:11:17] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:11:17] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:11:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2024-09-26 18:11:17] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:11:17] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-26 18:11:17] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:11:17] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:11:17] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:11:17] [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. [2024-09-26 18:11:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:11:18] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2024-09-26 18:11:18] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2024-09-26 18:11:18] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2024-09-26 18:11:27] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:11:27] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-26 18:11:27] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:11:27] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:11:27] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:11:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2024-09-26 18:11:27] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:11:27] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-26 18:11:27] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:11:27] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:11:27] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:11:27] [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. [2024-09-26 18:11:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:27] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:27] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:27] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:29] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:29] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:11:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:11:29] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:11:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:11:29] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`. [2024-09-26 18:11:29] [TRACE] [OmnipathR] Exporting object to RDS: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-09-26 18:11:30] [TRACE] [OmnipathR] Exported RDS to `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-09-26 18:11:30] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2024-09-26 18:11:30] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-26 18:11:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-26 18:11:30] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`. [2024-09-26 18:11:30] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-09-26 18:11:35] [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 [2024-09-26 18:11:41] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:11:41] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-26 18:11:41] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:11:41] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:11:41] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:11:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2024-09-26 18:11:41] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-09-26 18:11:41] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1. [2024-09-26 18:11:41] [TRACE] [OmnipathR] Cache file path: /media/volume/teran2_disk/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-09-26 18:11:41] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-09-26 18:11:41] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-09-26 18:11:41] [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. [2024-09-26 18:11:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:42] [TRACE] [OmnipathR] Loaded data from RDS `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-09-26 18:11:42] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-09-26 18:11:42] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-09-26 18:11:46] [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