############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR ### ############################################################################## ############################################################################## * checking for file ‘OmnipathR/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 [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-09 17:48:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-09 17:48:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-09 [2025-02-09 17:48:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-09 22:48:17 UTC; unix [2025-02-09 17:48:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6 [2025-02-09 17:48:41] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-09 17:48:41] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-09; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA] [2025-02-09 17:48:41] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-09 17:48:41] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-02-09 17:48:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Contains 1 files. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/private/tmp/RtmptOZqjg/Rinstb415620019a/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/private/tmp/RtmptOZqjg/Rinstb415620019a/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/private/tmp/RtmptOZqjg/Rinstb415620019a/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/private/tmp/RtmptOZqjg/Rinstb415620019a/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [TRACE] [OmnipathR] Cache locked: FALSE [2025-02-09 17:48:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2025-02-09 17:48:41] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:41] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-02-09 17:48:41] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-02-09 17:48:41] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-09 17:48:41] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-09 17:48:41] [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] [2025-02-09 17:48:42] [TRACE] [OmnipathR] HTTP 200 [2025-02-09 17:48:43] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-02-09 17:48:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:43] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-02-09 17:48:43] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-09 17:48:43] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-02-09 17:48:43] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-02-09 17:48:43] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-02-09 17:48:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:43] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-02-09 17:48:43] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-02-09 17:48:43] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-02-09 17:48:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-02-09 17:48:43] [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] [2025-02-09 17:48:44] [TRACE] [OmnipathR] Downloaded 108 Kb in 1.326145s from omabrowser.org (81.5 Kb/s); Redirect: 0s, DNS look up: 0.001073s, Connection: 0.00198s, Pretransfer: 0.609355s, First byte at: 0.693502s [2025-02-09 17:48:45] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-02-09 17:48:45] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-02-09 17:48:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:45] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-02-09 17:48:45] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-02-09 17:48:45] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:48:45] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:48:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:45] [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] [2025-02-09 17:48:48] [TRACE] [OmnipathR] Downloaded 2.2 Mb in 3.02209s from omnipathdb.org (733.3 Kb/s); Redirect: 0s, DNS look up: 0.02098s, Connection: 0.022003s, Pretransfer: 0.616945s, First byte at: 0.780131s [2025-02-09 17:48:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 17:48:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:48] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2025-02-09 17:48:48] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-02-09 17:48:49] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-02-09 17:48:49] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2025-02-09 17:48:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:48:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:48:49] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2025-02-09 17:48:54] [SUCCESS] [OmnipathR] Downloaded 128218 interactions. [2025-02-09 17:49:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-02-09 17:49:00] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:00] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:00] [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] [2025-02-09 17:49:02] [TRACE] [OmnipathR] Downloaded 906.3 Kb in 1.808237s from omnipathdb.org (501.2 Kb/s); Redirect: 0s, DNS look up: 0.001134s, Connection: 0.00222s, Pretransfer: 0.301849s, First byte at: 0.450177s [2025-02-09 17:49:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:02] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:02] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-02-09 17:49:02] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-02-09 17:49:02] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2025-02-09 17:49:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:02] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:04] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2025-02-09 17:49:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2025-02-09 17:49:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:05] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:05] [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] [2025-02-09 17:49:08] [TRACE] [OmnipathR] Downloaded 2.1 Mb in 2.490108s from omnipathdb.org (872.6 Kb/s); Redirect: 0s, DNS look up: 0.00099s, Connection: 0.001933s, Pretransfer: 0.151855s, First byte at: 0.303045s [2025-02-09 17:49:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:08] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-02-09 17:49:09] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-02-09 17:49:09] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-02-09 17:49:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:09] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:12] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2025-02-09 17:49:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2025-02-09 17:49:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:13] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:13] [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] [2025-02-09 17:49:15] [TRACE] [OmnipathR] Downloaded 1.4 Mb in 1.914265s from omnipathdb.org (773.3 Kb/s); Redirect: 0s, DNS look up: 0.001271s, Connection: 0.002224s, Pretransfer: 0.148233s, First byte at: 0.29475s [2025-02-09 17:49:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2025-02-09 17:49:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:16] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:16] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-02-09 17:49:16] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-02-09 17:49:16] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2025-02-09 17:49:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:16] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:16] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes. [2025-02-09 17:49:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-02-09 17:49:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:16] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 17:49:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:17] [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] [2025-02-09 17:49:19] [TRACE] [OmnipathR] Downloaded 1 Mb in 1.942244s from omnipathdb.org (552.5 Kb/s); Redirect: 0s, DNS look up: 0.0011s, Connection: 0.002044s, Pretransfer: 0.161668s, First byte at: 0.32292s [2025-02-09 17:49:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:19] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:19] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-02-09 17:49:20] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-02-09 17:49:20] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-02-09 17:49:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:20] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:20] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2025-02-09 17:49:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2025-02-09 17:49:20] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:20] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 17:49:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [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] [2025-02-09 17:49:21] [TRACE] [OmnipathR] Downloaded 60 bytes in 0.253546s from omnipathdb.org (236 bytes/s); Redirect: 0s, DNS look up: 0.001069s, Connection: 0.001969s, Pretransfer: 0.176818s, First byte at: 0.253495s [2025-02-09 17:49:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-02-09 17:49:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:21] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:21] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-02-09 17:49:21] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-02-09 17:49:21] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2025-02-09 17:49:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:21] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:21] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2025-02-09 17:49:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2025-02-09 17:49:21] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2025-02-09 17:49:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-02-09 17:49:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:21] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 17:49:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:22] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-02-09 17:49:22] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 17:49:22] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-02-09 17:49:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2025-02-09 17:49:23] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:23] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 17:49:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:23] [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] [2025-02-09 17:49:24] [TRACE] [OmnipathR] Downloaded 22.3 Kb in 0.411142s from omnipathdb.org (54.1 Kb/s); Redirect: 0s, DNS look up: 0.001128s, Connection: 0.001939s, Pretransfer: 0.16877s, First byte at: 0.335282s [2025-02-09 17:49:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-02-09 17:49:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:24] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:24] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-02-09 17:49:24] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-02-09 17:49:24] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2025-02-09 17:49:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:24] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:24] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records. [2025-02-09 17:49:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-02-09 17:49:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:24] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 17:49:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:25] [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] [2025-02-09 17:49:26] [TRACE] [OmnipathR] Downloaded 36.9 Kb in 0.468606s from omnipathdb.org (78.7 Kb/s); Redirect: 0s, DNS look up: 0.001118s, Connection: 0.001942s, Pretransfer: 0.163639s, First byte at: 0.319139s [2025-02-09 17:49:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:26] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:26] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-02-09 17:49:26] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-02-09 17:49:26] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2025-02-09 17:49:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:26] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:26] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records. [2025-02-09 17:49:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-02-09 17:49:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-02-09 17:49:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:26] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:26] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-02-09 17:49:26] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:49:30] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-02-09 17:49:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2025-02-09 17:49:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:30] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 17:49:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:31] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-02-09 17:49:31] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 17:49:31] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache. [2025-02-09 17:49:31] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:31] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:31] [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] [2025-02-09 17:49:37] [TRACE] [OmnipathR] Downloaded 6.1 Mb in 4.995925s from omnipathdb.org (1.2 Mb/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.002027s, Pretransfer: 0.160115s, First byte at: 0.318679s [2025-02-09 17:49:37] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2025-02-09 17:49:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:37] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:37] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-02-09 17:49:39] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-02-09 17:49:39] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2025-02-09 17:49:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:39] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:40] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records. [2025-02-09 17:49:40] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-02-09 17:49:40] [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. [2025-02-09 17:49:41] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2025-02-09 17:49:41] [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. [2025-02-09 17:49:41] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2025-02-09 17:49:41] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2025-02-09 17:49:41] [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. [2025-02-09 17:49:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 17:49:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:41] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:49:41] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:49:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-02-09 17:49:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2025-02-09 17:49:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2025-02-09 17:49:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2025-02-09 17:49:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2025-02-09 17:49:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2025-02-09 17:49:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2025-02-09 17:49:42] [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] [2025-02-09 17:49:42] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.227237s from omnipathdb.org (38.4 Kb/s); Redirect: 0s, DNS look up: 0.001027s, Connection: 0.001891s, Pretransfer: 0.152429s, First byte at: 0.226978s [2025-02-09 17:49:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2025-02-09 17:49:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:42] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:42] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-02-09 17:49:42] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-02-09 17:49:42] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2025-02-09 17:49:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:42] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2025-02-09 17:49:42] [SUCCESS] [OmnipathR] Downloaded 1098 records. [2025-02-09 17:49:42] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2025-02-09 17:49:42] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-02-09 17:49:42] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-02-09 17:49:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-09 17:49:42] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-02-09 17:49:42] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-02-09 17:49:42] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-02-09 17:49:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:49:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:49:42] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-02-09 17:49:42] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-02-09 17:49:42] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-02-09 17:49:42] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-02-09 17:49:42] [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] [2025-02-09 17:50:00] [TRACE] [OmnipathR] Downloaded 126.2 Kb in 17.152932s from rest.uniprot.org (7.4 Kb/s); Redirect: 0s, DNS look up: 0.018704s, Connection: 0.019748s, Pretransfer: 0.519875s, First byte at: 1.089402s [2025-02-09 17:50:00] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-02-09 17:50:00] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2025-02-09 17:50:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:50:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:50:00] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2025-02-09 17:50:00] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records [2025-02-09 17:50:01] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-02-09 17:50:01] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-02-09 17:50:01] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-02-09 17:50:01] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2025-02-09 17:50:01] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2025-02-09 17:50:01] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2025-02-09 17:50:01] [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. [2025-02-09 17:50:01] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2025-02-09 17:50:01] [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. [2025-02-09 17:50:01] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2025-02-09 17:50:01] [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. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2025-02-09 17:50:03] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2025-02-09 17:50:03] [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. [2025-02-09 17:50:03] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2025-02-09 17:50:03] [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. [2025-02-09 17:50:03] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2025-02-09 17:50:03] [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. [2025-02-09 17:50:04] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2025-02-09 17:50:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2025-02-09 17:50:04] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:50:04] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:50:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:50:04] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-02-09 17:50:04] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:50:08] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-02-09 17:50:08] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-02-09 17:50:08] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-02-09 17:50:08] [TRACE] [OmnipathR] BioMart query: [2025-02-09 17:50:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. Quitting from lines 176-179 [omnipath] (cosmos.Rmd) Error: processing vignette 'cosmos.Rmd' failed with diagnostics: not a namespace --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2025-02-09 17:50:08] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2025-02-09 17:50:08] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-02-09 17:50:08] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-02-09 17:50:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-09 17:50:08] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-02-09 17:50:08] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-02-09 17:50:08] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): loaded 20417 records from cache [2025-02-09 17:50:09] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2025-02-09 17:50:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-02-09 17:50:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-02-09 17:50:22] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:50:22] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:50:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:50:23] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-02-09 17:50:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 17:50:27] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. 2025-02-09 17:50:35.049 R[5636:127609390] XType: com.apple.fonts is not accessible. 2025-02-09 17:50:35.049 R[5636:127609390] XType: XTFontStaticRegistry is enabled. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2025-02-09 17:50:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2025-02-09 17:50:40] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 17:50:40] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 17:50:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:40] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:40] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:40] [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] [2025-02-09 17:50:44] [TRACE] [OmnipathR] Downloaded 3.5 Mb in 3.391545s from omnipathdb.org (1 Mb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.001865s, Pretransfer: 0.162368s, First byte at: 0.321913s [2025-02-09 17:50:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-02-09 17:50:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:50:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:50:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:50:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:50:45] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2025-02-09 17:50:45] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-02-09 17:50:47] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-02-09 17:50:47] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2025-02-09 17:50:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 17:50:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 17:50:47] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2025-02-09 17:50:47] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-02-09 17:51:15] [SUCCESS] [OmnipathR] Downloaded 134282 interactions. [2025-02-09 18:05:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2025-02-09 18:05:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:05:13] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:05:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:05:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:14] [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] [2025-02-09 18:05:17] [TRACE] [OmnipathR] Downloaded 1.9 Mb in 2.402604s from omnipathdb.org (791.1 Kb/s); Redirect: 0s, DNS look up: 0.001029s, Connection: 0.002164s, Pretransfer: 0.158739s, First byte at: 0.314134s [2025-02-09 18:05:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-02-09 18:05:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:18] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2025-02-09 18:05:18] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-02-09 18:05:18] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-02-09 18:05:18] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2025-02-09 18:05:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:18] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2025-02-09 18:05:18] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records. [2025-02-09 18:05:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2025-02-09 18:05:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:05:19] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:05:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:19] [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] [2025-02-09 18:05:19] [TRACE] [OmnipathR] Downloaded 5.1 Kb in 0.252477s from omnipathdb.org (20.2 Kb/s); Redirect: 0s, DNS look up: 0.001004s, Connection: 0.002175s, Pretransfer: 0.169687s, First byte at: 0.252412s [2025-02-09 18:05:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-02-09 18:05:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:20] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2025-02-09 18:05:20] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-02-09 18:05:20] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-02-09 18:05:20] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2025-02-09 18:05:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:20] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2025-02-09 18:05:20] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2025-02-09 18:05:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2025-02-09 18:05:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2025-02-09 18:05:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:05:26] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:05:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:27] [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] [2025-02-09 18:05:29] [TRACE] [OmnipathR] Downloaded 1.6 Mb in 2.327773s from omnipathdb.org (698.7 Kb/s); Redirect: 0s, DNS look up: 0.001121s, Connection: 0.002189s, Pretransfer: 0.162681s, First byte at: 0.322291s [2025-02-09 18:05:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:30] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2025-02-09 18:05:30] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-02-09 18:05:30] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-02-09 18:05:30] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2025-02-09 18:05:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:30] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2025-02-09 18:05:33] [SUCCESS] [OmnipathR] Downloaded 64485 interactions. [2025-02-09 18:05:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2025-02-09 18:05:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2025-02-09 18:05:41] [TRACE] [OmnipathR] Organism(s): 10090 [2025-02-09 18:05:41] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:05:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:05:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:42] [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] [2025-02-09 18:05:44] [TRACE] [OmnipathR] Downloaded 1.2 Mb in 1.885819s from omnipathdb.org (661 Kb/s); Redirect: 0s, DNS look up: 0.001264s, Connection: 0.002334s, Pretransfer: 0.157551s, First byte at: 0.312784s [2025-02-09 18:05:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:45] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2025-02-09 18:05:45] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-02-09 18:05:45] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-02-09 18:05:45] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2025-02-09 18:05:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:45] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2025-02-09 18:05:47] [SUCCESS] [OmnipathR] Downloaded 39742 interactions. [2025-02-09 18:05:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2025-02-09 18:05:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2025-02-09 18:05:47] [TRACE] [OmnipathR] Organism(s): 10116 [2025-02-09 18:05:47] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:05:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:48] [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] [2025-02-09 18:05:49] [TRACE] [OmnipathR] Downloaded 438.4 Kb in 1.386563s from omnipathdb.org (316.1 Kb/s); Redirect: 0s, DNS look up: 0.001213s, Connection: 0.002257s, Pretransfer: 0.152953s, First byte at: 0.305838s [2025-02-09 18:05:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:50] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2025-02-09 18:05:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-02-09 18:05:50] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-02-09 18:05:50] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2025-02-09 18:05:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:50] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2025-02-09 18:05:50] [SUCCESS] [OmnipathR] Downloaded 6869 interactions. [2025-02-09 18:05:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2025-02-09 18:05:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2025-02-09 18:05:51] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:05:51] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:05:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:05:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:51] [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] [2025-02-09 18:05:53] [TRACE] [OmnipathR] Downloaded 188.5 Kb in 1.094499s from omnipathdb.org (172.3 Kb/s); Redirect: 0s, DNS look up: 0.001152s, Connection: 0.002197s, Pretransfer: 0.153858s, First byte at: 0.303927s [2025-02-09 18:05:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:53] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2025-02-09 18:05:53] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-02-09 18:05:53] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-02-09 18:05:53] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2025-02-09 18:05:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:05:53] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2025-02-09 18:05:54] [SUCCESS] [OmnipathR] Downloaded 2834 interactions. [2025-02-09 18:05:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-02-09 18:05:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-02-09 18:05:54] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:05:54] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:05:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:54] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-02-09 18:05:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:05:58] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-02-09 18:06:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2025-02-09 18:06:00] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:00] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:00] [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] [2025-02-09 18:06:01] [TRACE] [OmnipathR] Downloaded 264.9 Kb in 1.216698s from omnipathdb.org (217.7 Kb/s); Redirect: 0s, DNS look up: 0.001162s, Connection: 0.002426s, Pretransfer: 0.169429s, First byte at: 0.336289s [2025-02-09 18:06:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-02-09 18:06:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:02] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:02] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-02-09 18:06:02] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-02-09 18:06:02] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2025-02-09 18:06:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:02] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:02] [SUCCESS] [OmnipathR] Downloaded 6127 interactions. [2025-02-09 18:06:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2025-02-09 18:06:02] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:02] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:03] [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] [2025-02-09 18:06:04] [TRACE] [OmnipathR] Downloaded 25.1 Kb in 0.366791s from omnipathdb.org (68.3 Kb/s); Redirect: 0s, DNS look up: 0.001118s, Connection: 0.002444s, Pretransfer: 0.149892s, First byte at: 0.29603s [2025-02-09 18:06:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:04] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:04] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-02-09 18:06:04] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-02-09 18:06:04] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2025-02-09 18:06:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:04] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:05] [SUCCESS] [OmnipathR] Downloaded 716 interactions. [2025-02-09 18:06:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2025-02-09 18:06:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:05] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:05] [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] [2025-02-09 18:06:05] [TRACE] [OmnipathR] Downloaded 2.2 Kb in 0.240157s from omnipathdb.org (9 Kb/s); Redirect: 0s, DNS look up: 0.001143s, Connection: 0.002483s, Pretransfer: 0.161815s, First byte at: 0.240103s [2025-02-09 18:06:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-02-09 18:06:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:06] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:06] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-02-09 18:06:06] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-02-09 18:06:06] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2025-02-09 18:06:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:06] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:06] [SUCCESS] [OmnipathR] Downloaded 32 interactions. [2025-02-09 18:06:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-02-09 18:06:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:07] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:07] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-02-09 18:06:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:09] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache. [2025-02-09 18:06:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-02-09 18:06:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-02-09 18:06:09] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:09] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:10] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-02-09 18:06:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:13] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2025-02-09 18:06:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2025-02-09 18:06:15] [TRACE] [OmnipathR] Organism(s): 10090 [2025-02-09 18:06:15] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:15] [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] [2025-02-09 18:06:17] [TRACE] [OmnipathR] Downloaded 446.1 Kb in 1.411667s from omnipathdb.org (316 Kb/s); Redirect: 0s, DNS look up: 0.001073s, Connection: 0.002317s, Pretransfer: 0.164032s, First byte at: 0.325724s [2025-02-09 18:06:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-02-09 18:06:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:18] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:18] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-02-09 18:06:18] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-02-09 18:06:18] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2025-02-09 18:06:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:18] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:19] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships. [2025-02-09 18:06:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2025-02-09 18:06:20] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:20] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:21] [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] [2025-02-09 18:06:22] [TRACE] [OmnipathR] Downloaded 270.4 Kb in 1.334641s from omnipathdb.org (202.6 Kb/s); Redirect: 0s, DNS look up: 0.001132s, Connection: 0.002334s, Pretransfer: 0.156331s, First byte at: 0.307096s [2025-02-09 18:06:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-02-09 18:06:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:23] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:23] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-02-09 18:06:23] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-02-09 18:06:23] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2025-02-09 18:06:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:23] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:23] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes. [2025-02-09 18:06:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations] [2025-02-09 18:06:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:27] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:27] [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] [2025-02-09 18:06:27] [TRACE] [OmnipathR] Downloaded 15 Kb in 0.322403s from omnipathdb.org (46.4 Kb/s); Redirect: 0s, DNS look up: 0.001094s, Connection: 0.002396s, Pretransfer: 0.163099s, First byte at: 0.322095s [2025-02-09 18:06:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-02-09 18:06:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:28] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:28] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`. [2025-02-09 18:06:28] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`. [2025-02-09 18:06:28] [INFO] [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1] [2025-02-09 18:06:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:28] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:28] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records. [2025-02-09 18:06:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2025-02-09 18:06:28] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:28] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:29] [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] [2025-02-09 18:06:29] [TRACE] [OmnipathR] Downloaded 5.8 Kb in 0.243826s from omnipathdb.org (23.8 Kb/s); Redirect: 0s, DNS look up: 0.000939s, Connection: 0.002206s, Pretransfer: 0.164587s, First byte at: 0.243764s [2025-02-09 18:06:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:30] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:30] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`. [2025-02-09 18:06:30] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`. [2025-02-09 18:06:30] [INFO] [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1] [2025-02-09 18:06:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:30] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:30] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2025-02-09 18:06:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2025-02-09 18:06:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:30] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:31] [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] [2025-02-09 18:06:31] [TRACE] [OmnipathR] Downloaded 3.8 Kb in 0.242759s from omnipathdb.org (15.5 Kb/s); Redirect: 0s, DNS look up: 0.001014s, Connection: 0.002117s, Pretransfer: 0.163069s, First byte at: 0.2426s [2025-02-09 18:06:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-02-09 18:06:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:32] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:32] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`. [2025-02-09 18:06:32] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`. [2025-02-09 18:06:32] [INFO] [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1] [2025-02-09 18:06:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:32] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:32] [SUCCESS] [OmnipathR] Downloaded 424 annotation records. [2025-02-09 18:06:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-02-09 18:06:32] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:32] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 18:06:33] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-02-09 18:06:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-02-09 18:06:33] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache. [2025-02-09 18:06:33] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:33] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-02-09 18:06:33] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-02-09 18:06:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary` [2025-02-09 18:06:33] [SUCCESS] [OmnipathR] Loaded 1098 records from cache. [2025-02-09 18:06:33] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:33] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:33] [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] [2025-02-09 18:06:37] [TRACE] [OmnipathR] Downloaded 4.7 Mb in 3.867092s from omnipathdb.org (1.2 Mb/s); Redirect: 0s, DNS look up: 0.000987s, Connection: 0.002275s, Pretransfer: 0.153855s, First byte at: 0.30607s [2025-02-09 18:06:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-02-09 18:06:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:38] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:38] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-02-09 18:06:40] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-02-09 18:06:40] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2025-02-09 18:06:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:40] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:40] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records. [2025-02-09 18:06:41] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-02-09 18:06:41] [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. [2025-02-09 18:06:41] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2025-02-09 18:06:41] [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. --- finished re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2025-02-09 18:06:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2025-02-09 18:06:43] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:43] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:44] [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] [2025-02-09 18:06:44] [TRACE] [OmnipathR] Downloaded 29.2 Kb in 0.407573s from omnipathdb.org (71.5 Kb/s); Redirect: 0s, DNS look up: 0.0011s, Connection: 0.002582s, Pretransfer: 0.172634s, First byte at: 0.330188s [2025-02-09 18:06:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-02-09 18:06:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:45] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:45] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-02-09 18:06:45] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-02-09 18:06:45] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2025-02-09 18:06:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:45] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:45] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2025-02-09 18:06:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-09 18:06:45] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2025-02-09 18:06:45] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-02-09 18:06:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2025-02-09 18:06:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:45] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:46] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-02-09 18:06:46] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-02-09 18:06:46] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-02-09 18:06:46] [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] [2025-02-09 18:06:46] [TRACE] [OmnipathR] Downloaded 157.2 Kb in 0.136187s from static-content.springer.com (1.1 Mb/s); Redirect: 0s, DNS look up: 0.019554s, Connection: 0.020707s, Pretransfer: 0.062532s, First byte at: 0.074745s [2025-02-09 18:06:46] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-02-09 18:06:46] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2025-02-09 18:06:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:46] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:46] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2025-02-09 18:06:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2025-02-09 18:06:47] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:47] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:47] [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] [2025-02-09 18:06:49] [TRACE] [OmnipathR] Downloaded 2.1 Mb in 2.55937s from omnipathdb.org (822 Kb/s); Redirect: 0s, DNS look up: 0.001246s, Connection: 0.002479s, Pretransfer: 0.154275s, First byte at: 0.305426s [2025-02-09 18:06:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-02-09 18:06:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:50] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2025-02-09 18:06:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-02-09 18:06:51] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-02-09 18:06:51] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2025-02-09 18:06:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:06:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:51] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2025-02-09 18:06:56] [SUCCESS] [OmnipathR] Downloaded 121170 interactions. [2025-02-09 18:06:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2025-02-09 18:06:57] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:06:57] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:06:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:06:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:06:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:06:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:06:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:06:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:06:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:06:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:06:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:06:57] [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] [2025-02-09 18:07:00] [TRACE] [OmnipathR] Downloaded 2.4 Mb in 2.733278s from omnipathdb.org (903.2 Kb/s); Redirect: 0s, DNS look up: 0.001355s, Connection: 0.002459s, Pretransfer: 0.168119s, First byte at: 0.332397s [2025-02-09 18:07:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-02-09 18:07:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:01] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:01] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-02-09 18:07:02] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-02-09 18:07:02] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2025-02-09 18:07:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:02] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:02] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records. [2025-02-09 18:07:03] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:03] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:03] [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] [2025-02-09 18:07:04] [TRACE] [OmnipathR] Downloaded 110.8 Kb in 0.790881s from omnipathdb.org (140 Kb/s); Redirect: 0s, DNS look up: 0.001077s, Connection: 0.001953s, Pretransfer: 0.163274s, First byte at: 0.325471s [2025-02-09 18:07:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-02-09 18:07:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:05] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:05] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-02-09 18:07:05] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-02-09 18:07:05] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2025-02-09 18:07:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:05] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:05] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records. [2025-02-09 18:07:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:05] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:05] [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] [2025-02-09 18:07:07] [TRACE] [OmnipathR] Downloaded 310.9 Kb in 1.241061s from omnipathdb.org (250.5 Kb/s); Redirect: 0s, DNS look up: 0.001198s, Connection: 0.002223s, Pretransfer: 0.161132s, First byte at: 0.319305s [2025-02-09 18:07:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:07] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:07] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-02-09 18:07:08] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-02-09 18:07:08] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2025-02-09 18:07:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:08] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:08] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records. [2025-02-09 18:07:08] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:08] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:08] [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] [2025-02-09 18:07:09] [TRACE] [OmnipathR] Downloaded 251.9 Kb in 1.24043s from omnipathdb.org (203.1 Kb/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.002104s, Pretransfer: 0.161929s, First byte at: 0.31941s [2025-02-09 18:07:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-02-09 18:07:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:10] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:10] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-02-09 18:07:10] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-02-09 18:07:10] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2025-02-09 18:07:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:10] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:10] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records. [2025-02-09 18:07:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:10] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:10] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-02-09 18:07:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:10] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-02-09 18:07:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:10] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:10] [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] [2025-02-09 18:07:12] [TRACE] [OmnipathR] Downloaded 157.9 Kb in 1.025589s from omnipathdb.org (153.9 Kb/s); Redirect: 0s, DNS look up: 0.001278s, Connection: 0.002529s, Pretransfer: 0.165495s, First byte at: 0.32801s [2025-02-09 18:07:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-02-09 18:07:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:12] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:12] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-02-09 18:07:13] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-02-09 18:07:13] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2025-02-09 18:07:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:13] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:13] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records. [2025-02-09 18:07:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:13] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:13] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-02-09 18:07:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:13] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-02-09 18:07:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:13] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:13] [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] [2025-02-09 18:07:14] [TRACE] [OmnipathR] Downloaded 306.2 Kb in 1.244882s from omnipathdb.org (246 Kb/s); Redirect: 0s, DNS look up: 0.001674s, Connection: 0.002968s, Pretransfer: 0.164332s, First byte at: 0.324898s [2025-02-09 18:07:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-02-09 18:07:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:15] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:15] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-02-09 18:07:15] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-02-09 18:07:15] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2025-02-09 18:07:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:15] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:15] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records. [2025-02-09 18:07:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:15] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:15] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-02-09 18:07:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-02-09 18:07:16] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2025-02-09 18:07:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2025-02-09 18:07:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2025-02-09 18:07:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:16] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:16] [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] [2025-02-09 18:07:18] [TRACE] [OmnipathR] Downloaded 1.5 Mb in 2.048484s from omnipathdb.org (748.5 Kb/s); Redirect: 0s, DNS look up: 0.001019s, Connection: 0.00223s, Pretransfer: 0.148456s, First byte at: 0.292219s [2025-02-09 18:07:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:19] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:19] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-02-09 18:07:19] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-02-09 18:07:19] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2025-02-09 18:07:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:19] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:21] [SUCCESS] [OmnipathR] Downloaded 30053 interactions. [2025-02-09 18:07:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2025-02-09 18:07:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:21] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:07:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:22] [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] [2025-02-09 18:07:22] [TRACE] [OmnipathR] Downloaded 13.1 Kb in 0.302286s from omnipathdb.org (43.3 Kb/s); Redirect: 0s, DNS look up: 0.001059s, Connection: 0.002353s, Pretransfer: 0.153023s, First byte at: 0.301958s [2025-02-09 18:07:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-02-09 18:07:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:23] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:23] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-02-09 18:07:23] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-02-09 18:07:23] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2025-02-09 18:07:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:23] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:23] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records. [2025-02-09 18:07:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2025-02-09 18:07:23] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:23] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:07:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:24] [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] [2025-02-09 18:07:24] [TRACE] [OmnipathR] Downloaded 12.1 Kb in 0.323194s from omnipathdb.org (37.4 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.001962s, Pretransfer: 0.152965s, First byte at: 0.322944s [2025-02-09 18:07:25] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-02-09 18:07:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:25] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:25] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-02-09 18:07:25] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-02-09 18:07:25] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2025-02-09 18:07:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:25] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:25] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records. [2025-02-09 18:07:27] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2025-02-09 18:07:27] [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. [2025-02-09 18:07:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2025-02-09 18:07:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:27] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:07:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:27] [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] [2025-02-09 18:07:28] [TRACE] [OmnipathR] Downloaded 11.7 Kb in 0.472859s from omnipathdb.org (24.8 Kb/s); Redirect: 0s, DNS look up: 0.001027s, Connection: 0.001934s, Pretransfer: 0.320771s, First byte at: 0.472529s [2025-02-09 18:07:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-02-09 18:07:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:29] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:29] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-02-09 18:07:29] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-02-09 18:07:29] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2025-02-09 18:07:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:29] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:29] [SUCCESS] [OmnipathR] Downloaded 322 interactions. [2025-02-09 18:07:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-02-09 18:07:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:29] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:07:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 18:07:30] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-02-09 18:07:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 18:07:30] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-02-09 18:07:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-02-09 18:07:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:30] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:31] [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] [2025-02-09 18:07:31] [TRACE] [OmnipathR] Downloaded 20.2 Kb in 0.32094s from omnipathdb.org (62.8 Kb/s); Redirect: 0s, DNS look up: 0.001171s, Connection: 0.002034s, Pretransfer: 0.162293s, First byte at: 0.320215s [2025-02-09 18:07:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:32] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2025-02-09 18:07:32] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-02-09 18:07:32] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-02-09 18:07:32] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2025-02-09 18:07:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-09 18:07:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:32] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2025-02-09 18:07:32] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records. [2025-02-09 18:07:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-02-09 18:07:34] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:34] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:07:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 18:07:35] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-02-09 18:07:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-02-09 18:07:35] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2025-02-09 18:07:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-02-09 18:07:36] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-09 18:07:36] [TRACE] [OmnipathR] Orthology targets: [2025-02-09 18:07:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-02-09 18:07:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-09 18:07:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:36] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-02-09 18:07:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-02-09 18:07:36] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘cosmos.Rmd’ Error: Vignette re-building failed. Execution halted