[ Started: 2025-02-02 12:46:21 CET ] [ decoupleR v2.9.7 for BioC-3.20 from https://github.com/saezlab/decoupleR@master (3a41229 2024-10-19 14:06:09) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘decoupleR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘decoupleR.Rmd’ using rmarkdown Quitting from lines 32-46 [vignette_setup] (decoupleR.Rmd) Error: processing vignette 'decoupleR.Rmd' failed with diagnostics: there is no package called 'AUCell' --- failed re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2025-02-02 12:46:29] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-02 12:46:29] [INFO] [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown)] [2025-02-02 12:46:29] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-02-02 12:46:29] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-02-02 12:46:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Contains 1 files. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [TRACE] [OmnipathR] Cache locked: FALSE [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:29] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-02-02 12:46:29] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-02-02 12:46:29] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:29] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:46:29] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:46:34] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:46:34] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:46:39] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:39] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:46:39] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:46:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-02-02 12:46:40] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:46:40] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:40] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2025-02-02 12:46:40] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2025-02-02 12:46:40] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:40] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:46:40] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:46:45] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:46:45] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:46:50] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:46:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:46:50] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:46:50] [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. [2025-02-02 12:46:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:46:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:46:50] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:46:50] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:46:50] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:46:52] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:52] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2025-02-02 12:46:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-02-02 12:46:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-02-02 12:46:54] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2025-02-02 12:46:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:46:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:46:54] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2025-02-02 12:46:54] [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 [2025-02-02 12:47:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-02 12:47:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:09] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:47:09] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:47:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:47:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:09] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3. [2025-02-02 12:47:09] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html [2025-02-02 12:47:09] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:09] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:09] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:14] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:14] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:19] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:19] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-02-02 12:47:19] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:47:19] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:47:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:47:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:19] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4. [2025-02-02 12:47:19] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html [2025-02-02 12:47:19] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:19] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:19] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:24] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:24] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:29] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:29] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:30] [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. [2025-02-02 12:47:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:47:31] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-02-02 12:47:31] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-02-02 12:47:31] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2025-02-02 12:47:36] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:47:36] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:47:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:47:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:36] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5. [2025-02-02 12:47:36] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html [2025-02-02 12:47:36] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:36] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:36] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:41] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:41] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:46] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:46] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-02-02 12:47:46] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:47:46] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:47:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:47:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:46] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6. [2025-02-02 12:47:46] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html [2025-02-02 12:47:46] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:46] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:46] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:51] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:51] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:56] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:47:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:47:56] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:47:56] [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. [2025-02-02 12:47:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:47:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:47:57] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:47:57] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:47:57] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:47:58] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:58] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`. [2025-02-02 12:47:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-02-02 12:47:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-02-02 12:47:58] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2025-02-02 12:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:47:58] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`. [2025-02-02 12:47:58] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-02-02 12:48:02] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any Quitting from lines 122-126 [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 [2025-02-02 12:48:06] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:48:06] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:48:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:48:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:48:06] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7. [2025-02-02 12:48:06] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html [2025-02-02 12:48:06] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:06] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:48:06] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:48:11] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:48:11] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:48:16] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:48:16] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:48:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-02-02 12:48:17] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-02 12:48:17] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-02 12:48:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-02 12:48:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-02 12:48:17] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8. [2025-02-02 12:48:17] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html [2025-02-02 12:48:17] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:17] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:48:17] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:48:22] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:48:22] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:48:27] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-02-02 12:48:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-02 12:48:27] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt [2025-02-02 12:48:27] [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. [2025-02-02 12:48:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:48:28] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-02-02 12:48:28] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-02-02 12:48:28] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-02-02 12:48:31] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any Quitting from lines 92-96 [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: ‘decoupleR.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-02-02 12:48:34 CET ]