[ Started: 2024-11-08 12:24:19 CET ] [ OmnipathR v3.15.1 for BioC-3.20 from https://github.com/saezlab/OmnipathR@master (4ffd9ec 2024-11-07 16:20:19) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Contains 1 files. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpA0r7OC/Rinst314a76384b335b/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpA0r7OC/Rinst314a76384b335b/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpA0r7OC/Rinst314a76384b335b/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpA0r7OC/Rinst314a76384b335b/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [TRACE] [OmnipathR] Cache locked: FALSE [2024-11-08 12:24:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2024-11-08 12:24:32] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:32] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-11-08 12:24:32] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-11-08 12:24:32] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:32] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:32] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:32] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:24:37] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:37] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:37] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:24:42] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:43] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:43] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 Quitting from lines 216-218 [network] (bioc_workshop.Rmd) Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 500 --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2024-11-08 12:24:43] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2024-11-08 12:24:43] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-11-08 12:24:43] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2024-11-08 12:24:43] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-11-08 12:24:43] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2024-11-08 12:24:43] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-11-08 12:24:43] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:24:43] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:24:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:24:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:43] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2024-11-08 12:24:43] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2024-11-08 12:24:43] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:43] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:43] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:43] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:24:48] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:48] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:48] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:24:53] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:53] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:53] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 Quitting from lines 176-179 [omnipath] (cosmos.Rmd) Error: processing vignette 'cosmos.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error: ! HTTP 500 --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2024-11-08 12:24:54] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2024-11-08 12:24:54] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2024-11-08 12:24:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:24:54] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:24:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:24:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:24:54] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3. [2024-11-08 12:24:54] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html [2024-11-08 12:24:54] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:54] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:54] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:54] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:24:59] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:24:59] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:24:59] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:25:04] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:05] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:05] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 Quitting from lines 67-69 [get] (db_manager.Rmd) Error: processing vignette 'db_manager.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error: ! HTTP 500 --- failed re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2024-11-08 12:25:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2024-11-08 12:25:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2024-11-08 12:25:05] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:25:05] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:25:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:25:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:25:05] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4. [2024-11-08 12:25:05] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html [2024-11-08 12:25:05] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:05] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:05] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:05] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:25:10] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:10] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:10] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:25:15] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:15] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:16] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 Quitting from lines 46-51 [unnamed-chunk-2] (drug_targets.Rmd) Error: processing vignette 'drug_targets.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 500 --- failed re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2024-11-08 12:25:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2024-11-08 12:25:16] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:25:16] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:25:16] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5. [2024-11-08 12:25:16] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html [2024-11-08 12:25:16] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:16] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:16] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:16] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:25:21] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:21] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:21] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:25:26] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:26] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:26] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd) Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 500 --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2024-11-08 12:25:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-11-08 12:25:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:25:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2024-11-08 12:25:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2024-11-08 12:25:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:25:28] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:25:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:25:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:25:28] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6. [2024-11-08 12:25:28] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html [2024-11-08 12:25:28] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:28] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:28] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:28] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:25:33] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:33] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:33] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:25:38] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:38] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:38] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 Quitting from lines 167-175 [interactions] (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 500 --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2024-11-08 12:25:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2024-11-08 12:25:38] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-11-08 12:25:38] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-11-08 12:25:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 12:25:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 12:25:38] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7. [2024-11-08 12:25:38] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html [2024-11-08 12:25:38] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:38] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:39] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:39] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 500 [2024-11-08 12:25:44] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:44] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:44] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 500 [2024-11-08 12:25:49] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-11-08 12:25:49] [WARN] [OmnipathR] HTTP 500 [2024-11-08 12:25:49] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 500 Quitting from lines 56-67 [tfcensus-op] (paths.Rmd) Error: processing vignette 'paths.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 500 --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘db_manager.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2024-11-08 12:25:49 CET ]