[ Started: 2025-02-08 19:54:05 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 [2025-02-08 19:54:13] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-08 19:54:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:13] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-08 19:54:13] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-04 17:36:54 UTC; omnipath [2025-02-08 19:54:13] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-08 19:54:13] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-04 17:36:55 UTC; unix [2025-02-08 19:54:13] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6 [2025-02-08 19:54:13] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-08 19:54:14] [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=2025-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-08 19:54:14] [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] [2025-02-08 19:54:14] [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 [2025-02-08 19:54:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Contains 1 files. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [TRACE] [OmnipathR] Cache locked: FALSE [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:14] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-02-08 19:54:14] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-02-08 19:54:14] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-08 19:54:14] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-08 19:54:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-08 19:54:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-08 19:54:14] [TRACE] [OmnipathR] HTTP 200 [2025-02-08 19:54:15] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-02-08 19:54:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:15] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-02-08 19:54:15] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-08 19:54:15] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-02-08 19:54:15] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-02-08 19:54:15] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-02-08 19:54:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:15] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-02-08 19:54:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-02-08 19:54:15] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-02-08 19:54:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-02-08 19:54:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-08 19:54:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-08 19:54:15] [TRACE] [OmnipathR] Downloaded 108 Kb in 0.107106s from omabrowser.org (1008.7 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.010576s, Pretransfer: 0.049189s, First byte at: 0.061665s [2025-02-08 19:54:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-02-08 19:54:15] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-02-08 19:54:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:15] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-02-08 19:54:15] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-02-08 19:54:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-02-08 19:54:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-08 19:54:15] [TRACE] [OmnipathR] Orthology targets: [2025-02-08 19:54:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-08 19:54:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-08 19:54:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-08 19:54:21] [TRACE] [OmnipathR] Downloaded 8.9 Mb in 4.655693s from omnipathdb.org (1.9 Mb/s); Redirect: 0s, DNS look up: 0.001037s, Connection: 0.018229s, Pretransfer: 0.068289s, First byte at: 3.941358s [2025-02-08 19:54:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:21] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2025-02-08 19:54:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-02-08 19:54:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-02-08 19:54:23] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2025-02-08 19:54:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:23] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2025-02-08 19:54:23] [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 [2025-02-08 19:54:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-08 19:54:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-02-08 19:54:39] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-08 19:54:39] [TRACE] [OmnipathR] Orthology targets: [2025-02-08 19:54:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-08 19:54:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-02-08 19:54:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-02-08 19:54:40] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2025-02-08 19:54:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-02-08 19:54:45] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-08 19:54:45] [TRACE] [OmnipathR] Orthology targets: [2025-02-08 19:54:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-08 19:54:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-08 19:54:46] [TRACE] [OmnipathR] Downloaded 1.7 Mb in 0.240538s from omnipathdb.org (6.9 Mb/s); Redirect: 0s, DNS look up: 0.001031s, Connection: 0.016549s, Pretransfer: 0.051482s, First byte at: 0.082048s [2025-02-08 19:54:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:54:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:46] [INFO] [OmnipathR] Cache item `76e3673f92890910194d45678b3125a5674920d6` version 1: status changed from `unknown` to `started`. [2025-02-08 19:54:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2025-02-08 19:54:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2025-02-08 19:54:46] [INFO] [OmnipathR] Download ready [key=76e3673f92890910194d45678b3125a5674920d6, version=1] [2025-02-08 19:54:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:46] [INFO] [OmnipathR] Cache item `76e3673f92890910194d45678b3125a5674920d6` version 1: status changed from `started` to `ready`. [2025-02-08 19:54:46] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-02-08 19:54:50] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2025-02-08 19:54:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,extra_attrs=TRUE,query_type=interactions,datasets=tf_mirna] [2025-02-08 19:54:50] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-08 19:54:50] [TRACE] [OmnipathR] Orthology targets: [2025-02-08 19:54:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-08 19:54:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-08 19:54:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-08 19:54:51] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.077758s from omnipathdb.org (122.1 Kb/s); Redirect: 0s, DNS look up: 0.000812s, Connection: 0.01997s, Pretransfer: 0.054473s, First byte at: 0.077538s [2025-02-08 19:54:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:54:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:51] [INFO] [OmnipathR] Cache item `911416570c2aaa914be32ebf7b85e1eb3d1ff162` version 1: status changed from `unknown` to `started`. [2025-02-08 19:54:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2025-02-08 19:54:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2025-02-08 19:54:51] [INFO] [OmnipathR] Download ready [key=911416570c2aaa914be32ebf7b85e1eb3d1ff162, version=1] [2025-02-08 19:54:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-08 19:54:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:54:51] [INFO] [OmnipathR] Cache item `911416570c2aaa914be32ebf7b85e1eb3d1ff162` version 1: status changed from `started` to `ready`. [2025-02-08 19:54:51] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-02-08 19:54:51] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-02-08 19:54:51] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2025-02-08 19:54:51] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2025-02-08 19:54:51] [SUCCESS] [OmnipathR] Downloaded 232 interactions. Warning: ggrepel: 754 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown [2025-02-08 19:55:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,extra_attrs=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-02-08 19:55:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-08 19:55:12] [TRACE] [OmnipathR] Orthology targets: [2025-02-08 19:55:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:55:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/76e3673f92890910194d45678b3125a5674920d6-1.rds`. [2025-02-08 19:55:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=extra_attrs,sources,references,curation_effort&loops=yes&license=academic` [2025-02-08 19:55:12] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-02-08 19:55:16] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache. [2025-02-08 19:55:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,extra_attrs=TRUE,query_type=interactions,datasets=tf_mirna] [2025-02-08 19:55:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-08 19:55:16] [TRACE] [OmnipathR] Orthology targets: [2025-02-08 19:55:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-08 19:55:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-08 19:55:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:55:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/911416570c2aaa914be32ebf7b85e1eb3d1ff162-1.rds`. [2025-02-08 19:55:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=extra_attrs,evidences,sources,references,curation_effort&license=academic` [2025-02-08 19:55:16] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-02-08 19:55:16] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-02-08 19:55:16] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2025-02-08 19:55:16] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2025-02-08 19:55:17] [SUCCESS] [OmnipathR] Loaded 232 interactions from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘tf_sc.Rmd’ SUMMARY: processing the following file failed: ‘decoupleR.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-02-08 19:55:25 CET ]