Multiple platform build/check report for BioC 3.21 - BUILD results for OmnipathR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4742
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4459
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BUILD results for OmnipathR on lconway

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: OmnipathR
Version: 3.15.11
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2025-03-18 17:53:27 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 18:14:35 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 1268.1 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

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###
### 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
[2025-03-18 17:53:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:53:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:54] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 17:53:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-18 17:53:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-18
[2025-03-18 17:53:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-18 21:53:29 UTC; unix
[2025-03-18 17:53:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-18 17:53:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-18 17:53:54] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); 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=2025-03-18; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-03-18 17:53:55] [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=10.44 2024-06-07; 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]
[2025-03-18 17:53:55] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.35.0(2025-03-18); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 1.9.1(2025-03-03); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-18); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-18 17:53:55] [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
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpfimJTh/Rinst1808625284cf5/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpfimJTh/Rinst1808625284cf5/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpfimJTh/Rinst1808625284cf5/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpfimJTh/Rinst1808625284cf5/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-03-18 17:53:55] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:55] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:53:55] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-03-18 17:53:55] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-18 17:53:55] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Downloaded 31 Kb in 8.503505s from www.ensembl.org (3.6 Kb/s); Redirect: 5.048641s, DNS look up: 0.046239s, Connection: 0.047822s, Pretransfer: 0.712951s, First byte at: 8.478222s
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Response headers: [date=Tue, 18 Mar 2025 21:54:04 GMT,content-type=text/html; charset=utf-8,content-length=31779,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Wed, 19 Mar 2025 21:42:35 GMT,set-cookie=ENSEMBL_WWW_SESSION=70732ee0fb947e5709b95fb0682902cb01be9a41111b07aafd5ba7ae; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Wed, 19 Mar 2025 21:42:35 GMT,set-cookie=ENSEMBL_WWW_SESSION=70732ee0fb947e5709b95fb0682902cb01be9a41111b07aafd5ba7ae; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-78.us-east-2.compute.internal]
[2025-03-18 17:54:04] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:04] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-18 17:54:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:05] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-18 17:54:05] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-03-18 17:54:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-03-18 17:54:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:06] [TRACE]   [OmnipathR] Downloaded 108 Kb in 1.436388s from omabrowser.org (75.2 Kb/s); Redirect: 0s, DNS look up: 0.015114s, Connection: 0.016041s, Pretransfer: 0.632748s, First byte at: 0.792s
[2025-03-18 17:54:06] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-18 17:54:06] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-03-18 17:54:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:06] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:06] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-03-18 17:54:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:06] [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`
[2025-03-18 17:54:06] [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`
[2025-03-18 17:54:06] [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`
[2025-03-18 17:54:06] [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`
[2025-03-18 17:54:06] [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`
[2025-03-18 17:54:06] [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`
[2025-03-18 17:54:06] [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`
[2025-03-18 17:54:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:09] [TRACE]   [OmnipathR] Downloaded 2.2 Mb in 2.835269s from omnipathdb.org (781.6 Kb/s); Redirect: 0s, DNS look up: 0.02046s, Connection: 0.021363s, Pretransfer: 0.381437s, First byte at: 0.55547s
[2025-03-18 17:54:10] [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`
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:10] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-03-18 17:54:10] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:10] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:15] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:22] [TRACE]   [OmnipathR] Downloaded 906.3 Kb in 1.79197s from omnipathdb.org (505.7 Kb/s); Redirect: 0s, DNS look up: 0.00098s, Connection: 0.00188s, Pretransfer: 0.168474s, First byte at: 0.338939s
[2025-03-18 17:54:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:23] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-03-18 17:54:23] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:23] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:25] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:26] [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`
[2025-03-18 17:54:26] [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`
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:30] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 4.167419s from omnipathdb.org (521.4 Kb/s); Redirect: 0s, DNS look up: 0.001042s, Connection: 0.001954s, Pretransfer: 0.160833s, First byte at: 1.939559s
[2025-03-18 17:54:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:30] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-18 17:54:31] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-18 17:54:31] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-03-18 17:54:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:31] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:34] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:37] [TRACE]   [OmnipathR] Downloaded 1.5 Mb in 2.133265s from omnipathdb.org (698.2 Kb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.001863s, Pretransfer: 0.159393s, First byte at: 0.313725s
[2025-03-18 17:54:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-03-18 17:54:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:37] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-03-18 17:54:38] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-03-18 17:54:38] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-03-18 17:54:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:38] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:38] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-03-18 17:54:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-03-18 17:54:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 17:54:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] Downloaded 1 Mb in 1.762604s from omnipathdb.org (608.8 Kb/s); Redirect: 0s, DNS look up: 0.001155s, Connection: 0.002118s, Pretransfer: 0.149147s, First byte at: 0.299649s
[2025-03-18 17:54:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:41] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-18 17:54:41] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:41] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:42] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-03-18 17:54:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-03-18 17:54:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.237103s from omnipathdb.org (253 bytes/s); Redirect: 0s, DNS look up: 0.001086s, Connection: 0.001987s, Pretransfer: 0.158346s, First byte at: 0.237052s
[2025-03-18 17:54:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:43] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-03-18 17:54:43] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:43] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:43] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-03-18 17:54:43] [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.
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-03-18 17:54:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 17:54:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:44] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-18 17:54:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 17:54:44] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-18 17:54:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-18 17:54:45] [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`
[2025-03-18 17:54:45] [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`
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-18 17:54:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-18 17:54:45] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Downloaded 22.3 Kb in 0.445074s from omnipathdb.org (50 Kb/s); Redirect: 0s, DNS look up: 0.001114s, Connection: 0.024062s, Pretransfer: 0.204332s, First byte at: 0.392099s
[2025-03-18 17:54:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-03-18 17:54:46] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:46] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Downloaded 36.9 Kb in 0.501497s from omnipathdb.org (73.6 Kb/s); Redirect: 0s, DNS look up: 0.001001s, Connection: 0.001915s, Pretransfer: 0.168435s, First byte at: 0.340553s
[2025-03-18 17:54:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:48] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-18 17:54:48] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:48] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-03-18 17:54:48] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:49] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-18 17:54:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:54:52] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-18 17:54:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:54:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-03-18 17:54:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-18 17:54:53] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 17:54:53] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:53] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:54:59] [TRACE]   [OmnipathR] Downloaded 6.1 Mb in 4.909494s from omnipathdb.org (1.2 Mb/s); Redirect: 0s, DNS look up: 0.00111s, Connection: 0.00195s, Pretransfer: 0.159721s, First byte at: 0.320467s
[2025-03-18 17:54:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-03-18 17:54:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:54:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:54:59] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:54:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-03-18 17:55:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-03-18 17:55:01] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-03-18 17:55:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:55:01] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-03-18 17:55:02] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-03-18 17:55:03] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-03-18 17:55:03] [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.
[2025-03-18 17:55:03] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2025-03-18 17:55:03] [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.
[2025-03-18 17:55:03] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-03-18 17:55:03] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-03-18 17:55:03] [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.
[2025-03-18 17:55:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 17:55:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.40218s from omnipathdb.org (21.7 Kb/s); Redirect: 0s, DNS look up: 0.001036s, Connection: 0.002117s, Pretransfer: 0.317133s, First byte at: 0.401939s
[2025-03-18 17:55:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:55:04] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-03-18 17:55:04] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:55:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:55:04] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-03-18 17:55:04] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-18 17:55:05] [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`.
[2025-03-18 17:55:05] [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`
[2025-03-18 17:55:05] [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`.
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:55:05] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-03-18 17:55:05] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-03-18 17:55:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:56:53] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2025-03-18 17:56:58] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-03-18 17:56:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:57:19] [TRACE]   [OmnipathR] Downloaded 126.2 Kb in 18.586176s from rest.uniprot.org (6.8 Kb/s); Redirect: 0s, DNS look up: 0.006719s, Connection: 0.007811s, Pretransfer: 0.55506s, First byte at: 1.148414s
[2025-03-18 17:57:19] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-03-18 17:57:19] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-03-18 17:57:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:57:19] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-03-18 17:57:20] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-03-18 17:57:20] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-03-18 17:57:20] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-03-18 17:57:20] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-03-18 17:57:20] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-03-18 17:57:20] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-03-18 17:57:22] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-03-18 17:57:22] [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.
[2025-03-18 17:57:22] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-03-18 17:57:22] [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.
[2025-03-18 17:57:22] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-03-18 17:57:23] [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
[2025-03-18 17:57:26] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-03-18 17:57:26] [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.
[2025-03-18 17:57:26] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-03-18 17:57:26] [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.
[2025-03-18 17:57:26] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-03-18 17:57:26] [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.
[2025-03-18 17:57:27] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-03-18 17:57:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:57:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-03-18 17:57:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:57:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:57:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:57:28] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-18 17:57:28] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:57:35] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-03-18 17:57:35] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:57:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:57:35] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-03-18 17:57:36] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Downloaded 346 bytes in 0.201112s from www.ensembl.org (1.7 Kb/s); Redirect: 0s, DNS look up: 0.002511s, Connection: 0.00358s, Pretransfer: 0.003661s, First byte at: 0.200951s
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 18 Mar 2025 21:57:36 GMT,Server=Apache,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',Keep-Alive=timeout=15, max=100,Transfer-Encoding=chunked,Content-Type=text/plain; charset=utf-8,Via=1.1 phswsa6.partners.org:80 (Cisco-WSA/15.2.0-164),Connection=keep-alive]
[2025-03-18 17:57:36] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-03-18 17:57:37] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-03-18 17:57:37] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-03-18 17:57:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:57:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:57:37] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-03-18 17:57:37] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-03-18 17:57:37] [WARN]    [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_113: DBI connect('database=ensembl_mart_113;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_113/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
[2025-03-18 17:57:37] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records

Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
The size of `nm` (2) must be compatible with the size of `x` (1).
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2025-03-18 17:57:38] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-03-18 17:57:38] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-03-18 17:57:38] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-03-18 17:57:38] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-18 17:57:38] [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`.
[2025-03-18 17:57:38] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-03-18 17:57:38] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): loaded 20417 records from cache
[2025-03-18 17:57:39] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2025-03-18 17:58:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:58:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-18 17:58:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:58:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-18 17:58:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:58:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:58:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:58:01] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-18 17:58:01] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 17:58:06] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
2025-03-18 17:58:17.862 R[1286:436016731] XType: com.apple.fonts is not accessible.
2025-03-18 17:58:17.862 R[1286:436016731] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2025-03-18 17:58:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 17:58:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-03-18 17:58:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 17:58:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 17:58:41] [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`
[2025-03-18 17:58:41] [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`
[2025-03-18 17:58:41] [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`
[2025-03-18 17:58:41] [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`
[2025-03-18 17:58:41] [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`
[2025-03-18 17:58:41] [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`
[2025-03-18 17:58:41] [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`
[2025-03-18 17:58:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 17:58:49] [TRACE]   [OmnipathR] Downloaded 3.5 Mb in 4.397855s from omnipathdb.org (812.2 Kb/s); Redirect: 0s, DNS look up: 0.000958s, Connection: 0.001914s, Pretransfer: 0.381645s, First byte at: 0.535603s
[2025-03-18 17:58:49] [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`
[2025-03-18 17:58:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:58:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:58:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:58:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:58:50] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-03-18 17:58:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-03-18 17:58:51] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-03-18 17:58:51] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-03-18 17:58:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 17:58:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 17:58:51] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-03-18 17:58:52] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-18 17:59:40] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-03-18 18:12:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-03-18 18:12:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:12:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:10] [TRACE]   [OmnipathR] Downloaded 1.9 Mb in 2.452051s from omnipathdb.org (775.2 Kb/s); Redirect: 0s, DNS look up: 0.001067s, Connection: 0.002149s, Pretransfer: 0.308452s, First byte at: 0.464865s
[2025-03-18 18:12:10] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-18 18:12:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:11] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-03-18 18:12:11] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-03-18 18:12:11] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-03-18 18:12:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:11] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:11] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-18 18:12:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-18 18:12:12] [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`
[2025-03-18 18:12:12] [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`
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-18 18:12:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:12] [TRACE]   [OmnipathR] Downloaded 5.1 Kb in 0.235197s from omnipathdb.org (21.7 Kb/s); Redirect: 0s, DNS look up: 0.001017s, Connection: 0.001874s, Pretransfer: 0.158334s, First byte at: 0.235135s
[2025-03-18 18:12:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:13] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-03-18 18:12:13] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:13] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:13] [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
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:20] [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`
[2025-03-18 18:12:20] [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`
[2025-03-18 18:12:20] [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`
[2025-03-18 18:12:20] [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`
[2025-03-18 18:12:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:20] [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`
[2025-03-18 18:12:20] [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`
[2025-03-18 18:12:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:22] [TRACE]   [OmnipathR] Downloaded 1.6 Mb in 1.930658s from omnipathdb.org (842.4 Kb/s); Redirect: 0s, DNS look up: 0.000973s, Connection: 0.002281s, Pretransfer: 0.150278s, First byte at: 0.296002s
[2025-03-18 18:12:22] [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`
[2025-03-18 18:12:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:22] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-03-18 18:12:23] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-03-18 18:12:23] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-03-18 18:12:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:23] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:26] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-03-18 18:12:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-03-18 18:12:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-03-18 18:12:34] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-03-18 18:12:34] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:12:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:35] [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`
[2025-03-18 18:12:35] [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`
[2025-03-18 18:12:35] [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`
[2025-03-18 18:12:35] [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`
[2025-03-18 18:12:35] [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`
[2025-03-18 18:12:35] [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`
[2025-03-18 18:12:35] [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`
[2025-03-18 18:12:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:37] [TRACE]   [OmnipathR] Downloaded 1.2 Mb in 2.012395s from omnipathdb.org (619.4 Kb/s); Redirect: 0s, DNS look up: 0.001179s, Connection: 0.002651s, Pretransfer: 0.164279s, First byte at: 0.321843s
[2025-03-18 18:12:37] [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`
[2025-03-18 18:12:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:37] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-03-18 18:12:38] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-03-18 18:12:38] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-03-18 18:12:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:38] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:40] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-03-18 18:12:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-03-18 18:12:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-03-18 18:12:40] [TRACE]   [OmnipathR] Organism(s): 10116
[2025-03-18 18:12:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:12:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:41] [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`
[2025-03-18 18:12:41] [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`
[2025-03-18 18:12:41] [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`
[2025-03-18 18:12:41] [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`
[2025-03-18 18:12:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:41] [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`
[2025-03-18 18:12:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:42] [TRACE]   [OmnipathR] Downloaded 438.4 Kb in 1.437842s from omnipathdb.org (304.9 Kb/s); Redirect: 0s, DNS look up: 0.00105s, Connection: 0.002109s, Pretransfer: 0.159311s, First byte at: 0.313244s
[2025-03-18 18:12:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:43] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-03-18 18:12:43] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:43] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:44] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-03-18 18:12:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-03-18 18:12:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-03-18 18:12:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:12:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:45] [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`
[2025-03-18 18:12:45] [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`
[2025-03-18 18:12:45] [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`
[2025-03-18 18:12:45] [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`
[2025-03-18 18:12:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:45] [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`
[2025-03-18 18:12:45] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:46] [TRACE]   [OmnipathR] Downloaded 188.5 Kb in 1.077982s from omnipathdb.org (174.9 Kb/s); Redirect: 0s, DNS look up: 0.001063s, Connection: 0.002154s, Pretransfer: 0.160594s, First byte at: 0.317096s
[2025-03-18 18:12:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:46] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-03-18 18:12:46] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-03-18 18:12:47] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:47] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:47] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:47] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-18 18:12:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:51] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-18 18:12:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-03-18 18:12:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:53] [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`
[2025-03-18 18:12:53] [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`
[2025-03-18 18:12:53] [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`
[2025-03-18 18:12:53] [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`
[2025-03-18 18:12:53] [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`
[2025-03-18 18:12:53] [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`
[2025-03-18 18:12:53] [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`
[2025-03-18 18:12:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:54] [TRACE]   [OmnipathR] Downloaded 264.9 Kb in 1.211516s from omnipathdb.org (218.6 Kb/s); Redirect: 0s, DNS look up: 0.001257s, Connection: 0.002177s, Pretransfer: 0.1586s, First byte at: 0.312069s
[2025-03-18 18:12:55] [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`
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:55] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-03-18 18:12:55] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:55] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:55] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:55] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:12:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:56] [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`
[2025-03-18 18:12:56] [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`
[2025-03-18 18:12:56] [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`
[2025-03-18 18:12:56] [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`
[2025-03-18 18:12:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:56] [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`
[2025-03-18 18:12:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] Downloaded 25.1 Kb in 0.417827s from omnipathdb.org (60 Kb/s); Redirect: 0s, DNS look up: 0.00105s, Connection: 0.002405s, Pretransfer: 0.172802s, First byte at: 0.33684s
[2025-03-18 18:12:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:57] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-03-18 18:12:57] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:57] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:57] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2025-03-18 18:12:58] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:12:58] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-03-18 18:12:58] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:12:58] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:12:58] [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`
[2025-03-18 18:12:58] [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`
[2025-03-18 18:12:58] [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`
[2025-03-18 18:12:58] [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`
[2025-03-18 18:12:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-03-18 18:12:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-03-18 18:12:58] [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`
[2025-03-18 18:12:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:12:58] [TRACE]   [OmnipathR] Downloaded 2.2 Kb in 0.237819s from omnipathdb.org (9.1 Kb/s); Redirect: 0s, DNS look up: 0.000995s, Connection: 0.00202s, Pretransfer: 0.15999s, First byte at: 0.237763s
[2025-03-18 18:12:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:59] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-03-18 18:12:59] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:12:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:12:59] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-03-18 18:12:59] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:00] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-03-18 18:13:00] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:02] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache.
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:02] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-18 18:13:02] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:06] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-18 18:13:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2025-03-18 18:13:07] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-03-18 18:13:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:08] [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`
[2025-03-18 18:13:08] [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`
[2025-03-18 18:13:08] [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`
[2025-03-18 18:13:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:10] [TRACE]   [OmnipathR] Downloaded 446.1 Kb in 1.618976s from omnipathdb.org (275.5 Kb/s); Redirect: 0s, DNS look up: 0.001063s, Connection: 0.00213s, Pretransfer: 0.161456s, First byte at: 0.3184s
[2025-03-18 18:13:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:11] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-03-18 18:13:11] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:11] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:12] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:15] [TRACE]   [OmnipathR] Downloaded 279.5 Kb in 1.304456s from omnipathdb.org (214.3 Kb/s); Redirect: 0s, DNS look up: 0.001077s, Connection: 0.002437s, Pretransfer: 0.158348s, First byte at: 0.311092s
[2025-03-18 18:13:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:16] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-03-18 18:13:16] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:16] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:16] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2025-03-18 18:13:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:20] [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]
[2025-03-18 18:13:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:20] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:20] [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`
[2025-03-18 18:13:20] [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`
[2025-03-18 18:13:20] [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`
[2025-03-18 18:13:20] [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`
[2025-03-18 18:13:20] [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`
[2025-03-18 18:13:20] [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`
[2025-03-18 18:13:20] [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`
[2025-03-18 18:13:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:20] [TRACE]   [OmnipathR] Downloaded 15 Kb in 0.352977s from omnipathdb.org (42.4 Kb/s); Redirect: 0s, DNS look up: 0.001173s, Connection: 0.002117s, Pretransfer: 0.162537s, First byte at: 0.352575s
[2025-03-18 18:13:21] [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`
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:21] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-03-18 18:13:21] [INFO]    [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1]
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:21] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:21] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records.
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:22] [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`
[2025-03-18 18:13:22] [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`
[2025-03-18 18:13:22] [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`
[2025-03-18 18:13:22] [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`
[2025-03-18 18:13:22] [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`
[2025-03-18 18:13:22] [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`
[2025-03-18 18:13:22] [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`
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:22] [TRACE]   [OmnipathR] Downloaded 5.8 Kb in 0.236325s from omnipathdb.org (24.6 Kb/s); Redirect: 0s, DNS look up: 0.001132s, Connection: 0.002059s, Pretransfer: 0.159623s, First byte at: 0.236266s
[2025-03-18 18:13:23] [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`
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:23] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-03-18 18:13:23] [INFO]    [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1]
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:23] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:23] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2025-03-18 18:13:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2025-03-18 18:13:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:24] [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`
[2025-03-18 18:13:24] [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`
[2025-03-18 18:13:24] [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`
[2025-03-18 18:13:24] [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`
[2025-03-18 18:13:24] [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`
[2025-03-18 18:13:24] [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`
[2025-03-18 18:13:24] [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`
[2025-03-18 18:13:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] Downloaded 3.8 Kb in 0.241724s from omnipathdb.org (15.6 Kb/s); Redirect: 0s, DNS look up: 0.001062s, Connection: 0.001995s, Pretransfer: 0.162607s, First byte at: 0.241486s
[2025-03-18 18:13:25] [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`
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:25] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-03-18 18:13:25] [INFO]    [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1]
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:25] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:25] [SUCCESS] [OmnipathR] Downloaded 424 annotation records.
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-18 18:13:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-18 18:13:26] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-03-18 18:13:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-03-18 18:13:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2025-03-18 18:13:27] [SUCCESS] [OmnipathR] Loaded 1098 records from cache.
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:31] [TRACE]   [OmnipathR] Downloaded 4.7 Mb in 3.789715s from omnipathdb.org (1.3 Mb/s); Redirect: 0s, DNS look up: 0.000977s, Connection: 0.001762s, Pretransfer: 0.149281s, First byte at: 0.300067s
[2025-03-18 18:13:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-18 18:13:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:32] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-03-18 18:13:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-03-18 18:13:33] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2025-03-18 18:13:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:33] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:34] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2025-03-18 18:13:34] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-03-18 18:13:34] [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.
[2025-03-18 18:13:35] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2025-03-18 18:13:35] [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
[2025-03-18 18:13:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-03-18 18:13:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:38] [TRACE]   [OmnipathR] Downloaded 29.2 Kb in 0.39739s from omnipathdb.org (73.4 Kb/s); Redirect: 0s, DNS look up: 0.001042s, Connection: 0.002035s, Pretransfer: 0.161449s, First byte at: 0.321979s
[2025-03-18 18:13:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:39] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-03-18 18:13:39] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:39] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:39] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-03-18 18:13:39] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-03-18 18:13:39] [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`.
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:39] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-03-18 18:13:39] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-03-18 18:13:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:40] [TRACE]   [OmnipathR] Downloaded 157.2 Kb in 0.265595s from static-content.springer.com (591.9 Kb/s); Redirect: 0s, DNS look up: 0.015591s, Connection: 0.016701s, Pretransfer: 0.061268s, First byte at: 0.197737s
[2025-03-18 18:13:40] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-03-18 18:13:40] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-03-18 18:13:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:40] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:40] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-03-18 18:13:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-03-18 18:13:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:41] [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`
[2025-03-18 18:13:41] [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`
[2025-03-18 18:13:41] [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`
[2025-03-18 18:13:41] [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`
[2025-03-18 18:13:41] [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`
[2025-03-18 18:13:41] [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`
[2025-03-18 18:13:41] [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`
[2025-03-18 18:13:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:44] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 2.822393s from omnipathdb.org (745.4 Kb/s); Redirect: 0s, DNS look up: 0.001126s, Connection: 0.002017s, Pretransfer: 0.167917s, First byte at: 0.335853s
[2025-03-18 18:13:44] [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`
[2025-03-18 18:13:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:44] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-03-18 18:13:45] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-03-18 18:13:45] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-03-18 18:13:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:45] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:50] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-03-18 18:13:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:13:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-03-18 18:13:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:13:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-18 18:13:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-18 18:13:51] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-18 18:13:51] [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`
[2025-03-18 18:13:51] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-18 18:13:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-18 18:13:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-18 18:13:51] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:54] [TRACE]   [OmnipathR] Downloaded 2.4 Mb in 2.662007s from omnipathdb.org (927.4 Kb/s); Redirect: 0s, DNS look up: 0.001026s, Connection: 0.002122s, Pretransfer: 0.159494s, First byte at: 0.318936s
[2025-03-18 18:13:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-18 18:13:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:55] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-03-18 18:13:56] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-03-18 18:13:56] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-03-18 18:13:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:56] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:56] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-03-18 18:13:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:13:58] [TRACE]   [OmnipathR] Downloaded 110.8 Kb in 0.983605s from omnipathdb.org (112.6 Kb/s); Redirect: 0s, DNS look up: 0.001174s, Connection: 0.002232s, Pretransfer: 0.171144s, First byte at: 0.341375s
[2025-03-18 18:13:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:59] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-03-18 18:13:59] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:13:59] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-03-18 18:13:59] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:13:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:13:59] [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`
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:13:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:13:59] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:01] [TRACE]   [OmnipathR] Downloaded 310.9 Kb in 1.4219s from omnipathdb.org (218.6 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.001978s, Pretransfer: 0.155288s, First byte at: 0.312787s
[2025-03-18 18:14:01] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:14:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:01] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-18 18:14:02] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:02] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:02] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:03] [TRACE]   [OmnipathR] Downloaded 251.9 Kb in 1.19464s from omnipathdb.org (210.9 Kb/s); Redirect: 0s, DNS look up: 0.000899s, Connection: 0.001908s, Pretransfer: 0.165241s, First byte at: 0.335913s
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:04] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:14:04] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:05] [TRACE]   [OmnipathR] Downloaded 157.9 Kb in 0.978785s from omnipathdb.org (161.3 Kb/s); Redirect: 0s, DNS look up: 0.001161s, Connection: 0.004765s, Pretransfer: 0.15749s, First byte at: 0.312663s
[2025-03-18 18:14:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:06] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-03-18 18:14:06] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:06] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:06] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:14:06] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-18 18:14:06] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:14:07] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-03-18 18:14:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:08] [TRACE]   [OmnipathR] Downloaded 306.2 Kb in 1.297269s from omnipathdb.org (236 Kb/s); Redirect: 0s, DNS look up: 0.001105s, Connection: 0.002015s, Pretransfer: 0.158172s, First byte at: 0.320668s
[2025-03-18 18:14:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:09] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-03-18 18:14:09] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:09] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:09] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-18 18:14:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-18 18:14:09] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-03-18 18:14:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:10] [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`
[2025-03-18 18:14:10] [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`
[2025-03-18 18:14:10] [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`
[2025-03-18 18:14:10] [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`
[2025-03-18 18:14:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-03-18 18:14:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-03-18 18:14:10] [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`
[2025-03-18 18:14:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:13] [TRACE]   [OmnipathR] Downloaded 1.5 Mb in 2.981869s from omnipathdb.org (514.2 Kb/s); Redirect: 0s, DNS look up: 0.00108s, Connection: 0.002028s, Pretransfer: 0.316564s, First byte at: 0.477422s
[2025-03-18 18:14:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-03-18 18:14:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:13] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-03-18 18:14:14] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-03-18 18:14:14] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-03-18 18:14:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:14] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:15] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:17] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.320816s from omnipathdb.org (40.8 Kb/s); Redirect: 0s, DNS look up: 0.001209s, Connection: 0.002205s, Pretransfer: 0.161752s, First byte at: 0.320478s
[2025-03-18 18:14:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-18 18:14:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:17] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-03-18 18:14:18] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:18] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:18] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:18] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:19] [TRACE]   [OmnipathR] Downloaded 12.1 Kb in 0.533959s from omnipathdb.org (22.6 Kb/s); Redirect: 0s, DNS look up: 0.001148s, Connection: 0.001984s, Pretransfer: 0.367354s, First byte at: 0.533701s
[2025-03-18 18:14:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:20] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-03-18 18:14:20] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:20] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:20] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-03-18 18:14:22] [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.
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:22] [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`
[2025-03-18 18:14:22] [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`
[2025-03-18 18:14:22] [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`
[2025-03-18 18:14:22] [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`
[2025-03-18 18:14:22] [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`
[2025-03-18 18:14:22] [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`
[2025-03-18 18:14:22] [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`
[2025-03-18 18:14:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:23] [TRACE]   [OmnipathR] Downloaded 11.7 Kb in 0.322094s from omnipathdb.org (36.3 Kb/s); Redirect: 0s, DNS look up: 0.001058s, Connection: 0.001902s, Pretransfer: 0.162576s, First byte at: 0.321874s
[2025-03-18 18:14:23] [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`
[2025-03-18 18:14:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:23] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-03-18 18:14:24] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:24] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:24] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 18:14:25] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-18 18:14:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 18:14:25] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-03-18 18:14:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-03-18 18:14:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:25] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-18 18:14:26] [TRACE]   [OmnipathR] Downloaded 20.2 Kb in 0.31542s from omnipathdb.org (63.9 Kb/s); Redirect: 0s, DNS look up: 0.00105s, Connection: 0.001917s, Pretransfer: 0.157712s, First byte at: 0.314963s
[2025-03-18 18:14:27] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:27] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-03-18 18:14:27] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 18:14:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:27] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-03-18 18:14:27] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-03-18 18:14:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-03-18 18:14:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-18 18:14:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-18 18:14:30] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-18 18:14:30] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-18 18:14:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-18 18:14:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 18:14:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:31] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-03-18 18:14:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-18 18:14:31] [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