| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-17 11:41 -0400 (Mon, 17 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| 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 | ||||
| Package 1469/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.15.11 (landing page) Denes Turei
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.15.11 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR |
| StartedAt: 2025-03-17 00:59:03 -0000 (Mon, 17 Mar 2025) |
| EndedAt: 2025-03-17 01:27:15 -0000 (Mon, 17 Mar 2025) |
| EllapsedTime: 1692.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
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* 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
[2025-03-17 00:59:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:45] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 00:59:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-17 00:59:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-16
[2025-03-17 00:59:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-17 00:59:07 UTC; unix
[2025-03-17 00:59:45] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-17 00:59:45] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-17 00:59:46] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA]
[2025-03-17 00:59:46] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-03-17 00:59:46] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.35.0(2025-03-16); 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(2025-03-16); 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)
[2025-03-17 00:59:46] [INFO] [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/RtmpZsKlwg/Rinst3e7e34380f9ce3/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 00:59:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/RtmpZsKlwg/Rinst3e7e34380f9ce3/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 00:59:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/RtmpZsKlwg/Rinst3e7e34380f9ce3/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 00:59:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/RtmpZsKlwg/Rinst3e7e34380f9ce3/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 00:59:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-03-17 00:59:46] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-03-17 00:59:47] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:47] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:47] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-03-17 00:59:47] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-03-17 00:59:47] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-03-17 00:59:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 00:59:47] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-03-17 00:59:47] [TRACE] [OmnipathR] Sending HTTP request.
[2025-03-17 00:59:48] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-03-17 00:59:48] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 1.15855s from www.ensembl.org (26.7 Kb/s); Redirect: 1.054085s, DNS look up: 0.272144s, Connection: 0.4573s, Pretransfer: 0.833355s, First byte at: 1.155382s
[2025-03-17 00:59:48] [TRACE] [OmnipathR] Response headers: [content-type=text/html; charset=utf-8,content-length=31649,date=Mon, 17 Mar 2025 01:00:41 GMT,x-nginx-machine=ip-10-25-26-93.ap-southeast-1.compute.internal,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Tue, 18 Mar 2025 00:50:31 GMT,set-cookie=ENSEMBL_WWW_SESSION=e4e3f1bbf501ba650f184c7668268bd7083ba3b6c702a6a0007b162e; 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=Tue, 18 Mar 2025 00:50:31 GMT,set-cookie=ENSEMBL_WWW_SESSION=e4e3f1bbf501ba650f184c7668268bd7083ba3b6c702a6a0007b162e; 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-cache=Miss from cloudfront,via=1.1 2ffad71acc1fd359f7575ee84d8a56dc.cloudfront.net (CloudFront),x-amz-cf-pop=SIN2-P4,x-amz-cf-id=uLW_lnmDGVCjE8TTfhShy0LCDJS-kWJo5y48obJ0Pa5dhRCQMxkDYg==,vary=Origin]
[2025-03-17 00:59:48] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-03-17 00:59:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:48] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-17 00:59:49] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:49] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-17 00:59:49] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-03-17 00:59:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 00:59:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 00:59:51] [TRACE] [OmnipathR] Downloaded 108 Kb in 2.187504s from omabrowser.org (49.4 Kb/s); Redirect: 0s, DNS look up: 0.177332s, Connection: 0.511194s, Pretransfer: 0.84925s, First byte at: 1.187659s
[2025-03-17 00:59:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-17 00:59:52] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-03-17 00:59:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:52] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-03-17 00:59:52] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-03-17 00:59:52] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 00:59:52] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 00:59:52] [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`
[2025-03-17 00:59:52] [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`
[2025-03-17 00:59:52] [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`
[2025-03-17 00:59:52] [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`
[2025-03-17 00:59:52] [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`
[2025-03-17 00:59:52] [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`
[2025-03-17 00:59:52] [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`
[2025-03-17 00:59:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 00:59:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 00:59:55] [TRACE] [OmnipathR] Downloaded 2.2 Mb in 1.882392s from omnipathdb.org (1.1 Mb/s); Redirect: 0s, DNS look up: 0.012751s, Connection: 0.179314s, Pretransfer: 0.349532s, First byte at: 0.684812s
[2025-03-17 00:59:55] [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`
[2025-03-17 00:59:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:55] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-03-17 00:59:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-03-17 00:59:56] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-03-17 00:59:56] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-03-17 00:59:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 00:59:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 00:59:56] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:03] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:12] [TRACE] [OmnipathR] Downloaded 906.3 Kb in 1.680311s from omnipathdb.org (539.3 Kb/s); Redirect: 0s, DNS look up: 0.011626s, Connection: 0.178238s, Pretransfer: 0.350484s, First byte at: 0.684828s
[2025-03-17 01:00:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:13] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-03-17 01:00:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-03-17 01:00:13] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-03-17 01:00:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:13] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:15] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:17] [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`
[2025-03-17 01:00:17] [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`
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:19] [TRACE] [OmnipathR] Downloaded 2.1 Mb in 2.587946s from omnipathdb.org (839.6 Kb/s); Redirect: 0s, DNS look up: 0.042661s, Connection: 0.20865s, Pretransfer: 0.378444s, First byte at: 0.709678s
[2025-03-17 01:00:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:20] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-17 01:00:20] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-17 01:00:20] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-03-17 01:00:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:20] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:25] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:25] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:28] [TRACE] [OmnipathR] Downloaded 1.5 Mb in 1.83148s from omnipathdb.org (813.3 Kb/s); Redirect: 0s, DNS look up: 0.008043s, Connection: 0.173395s, Pretransfer: 0.342693s, First byte at: 0.675423s
[2025-03-17 01:00:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-03-17 01:00:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:28] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-03-17 01:00:29] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-03-17 01:00:29] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-03-17 01:00:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:29] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:29] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-03-17 01:00:29] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-03-17 01:00:29] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:29] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:00:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:30] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:32] [TRACE] [OmnipathR] Downloaded 1 Mb in 1.507252s from omnipathdb.org (712 Kb/s); Redirect: 0s, DNS look up: 0.00833s, Connection: 0.17359s, Pretransfer: 0.343127s, First byte at: 0.677725s
[2025-03-17 01:00:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:33] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-17 01:00:33] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:33] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:33] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:33] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:00:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:35] [TRACE] [OmnipathR] Downloaded 60 bytes in 0.530126s from omnipathdb.org (113 bytes/s); Redirect: 0s, DNS look up: 0.009981s, Connection: 0.177574s, Pretransfer: 0.356742s, First byte at: 0.530084s
[2025-03-17 01:00:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:36] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-03-17 01:00:36] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:36] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:36] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-03-17 01:00:36] [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.
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:36] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:00:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:38] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-17 01:00:38] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:00:38] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-03-17 01:00:38] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-03-17 01:00:38] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:38] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:00:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-17 01:00:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-17 01:00:40] [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`
[2025-03-17 01:00:40] [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`
[2025-03-17 01:00:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-17 01:00:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-17 01:00:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-17 01:00:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:40] [TRACE] [OmnipathR] Downloaded 22.3 Kb in 0.693182s from omnipathdb.org (32.1 Kb/s); Redirect: 0s, DNS look up: 0.003908s, Connection: 0.171401s, Pretransfer: 0.345852s, First byte at: 0.682991s
[2025-03-17 01:00:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:41] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-03-17 01:00:41] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:41] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:41] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:41] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:00:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:43] [TRACE] [OmnipathR] Downloaded 36.9 Kb in 0.679312s from omnipathdb.org (54.3 Kb/s); Redirect: 0s, DNS look up: 0.00346s, Connection: 0.1704s, Pretransfer: 0.340903s, First byte at: 0.678459s
[2025-03-17 01:00:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:44] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-17 01:00:44] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:44] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-03-17 01:00:44] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-17 01:00:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:00:49] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-17 01:00:49] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:00:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-03-17 01:00:49] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:49] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:00:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-17 01:00:50] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:00:50] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:00:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:00:56] [TRACE] [OmnipathR] Downloaded 6.1 Mb in 4.470152s from omnipathdb.org (1.4 Mb/s); Redirect: 0s, DNS look up: 0.000741s, Connection: 0.168132s, Pretransfer: 0.340681s, First byte at: 0.675896s
[2025-03-17 01:00:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-03-17 01:00:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:56] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:00:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-03-17 01:00:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-03-17 01:00:59] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-03-17 01:00:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:00:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:00:59] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-03-17 01:01:00] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-03-17 01:01:01] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-03-17 01:01:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-03-17 01:01:01] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`.
[2025-03-17 01:01:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-03-17 01:01:01] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-03-17 01:01:01] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-03-17 01:01:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:01:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:01:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-03-17 01:01:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:01:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:01:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:01:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:01:03] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.507152s from omnipathdb.org (17.2 Kb/s); Redirect: 0s, DNS look up: 0.00072s, Connection: 0.168672s, Pretransfer: 0.339099s, First byte at: 0.506919s
[2025-03-17 01:01:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:01:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:03] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:01:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-03-17 01:01:03] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-03-17 01:01:03] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-03-17 01:01:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:03] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-03-17 01:01:03] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-03-17 01:01:04] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-03-17 01:01:04] [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`.
[2025-03-17 01:01:04] [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`
[2025-03-17 01:01:04] [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`.
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:04] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-03-17 01:01:04] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-03-17 01:01:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:01:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:01:22] [TRACE] [OmnipathR] Downloaded 126.2 Kb in 17.833242s from rest.uniprot.org (7.1 Kb/s); Redirect: 0s, DNS look up: 0.006899s, Connection: 0.191038s, Pretransfer: 0.568754s, First byte at: 1.241922s
[2025-03-17 01:01:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-03-17 01:01:22] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-03-17 01:01:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:22] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-03-17 01:01:22] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-03-17 01:01:23] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-03-17 01:01:23] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-03-17 01:01:23] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-03-17 01:01:23] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-03-17 01:01:23] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-03-17 01:01:23] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-03-17 01:01:23] [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.
[2025-03-17 01:01:23] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-03-17 01:01:23] [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.
[2025-03-17 01:01:23] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-03-17 01:01:23] [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
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-03-17 01:01:25] [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.
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-03-17 01:01:25] [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.
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-03-17 01:01:25] [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.
[2025-03-17 01:01:25] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:01:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-17 01:01:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:01:30] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-17 01:01:30] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-03-17 01:01:30] [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>
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-03-17 01:01:30] [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`.
[2025-03-17 01:01:30] [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`
[2025-03-17 01:01:30] [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`.
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:30] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-03-17 01:01:30] [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`
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-17 01:01:30] [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`
[2025-03-17 01:01:30] [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`.
[2025-03-17 01:01:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-03-17 01:01:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:01:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-03-17 01:01:30] [TRACE] [OmnipathR] Sending HTTP request.
[2025-03-17 01:01:31] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-03-17 01:01:31] [TRACE] [OmnipathR] Downloaded 346 bytes in 0.971471s from www.ensembl.org (356 bytes/s); Redirect: 0s, DNS look up: 0.545105s, Connection: 0.72495s, Pretransfer: 0.725053s, First byte at: 0.971426s
[2025-03-17 01:01:31] [TRACE] [OmnipathR] Response headers: [Date=Mon, 17 Mar 2025 01:02:24 GMT,Server=Apache,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',Transfer-Encoding=chunked,Content-Type=text/plain; charset=utf-8]
[2025-03-17 01:01:31] [TRACE] [OmnipathR] Calling reader callback on response.
[2025-03-17 01:01:32] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-03-17 01:01:32] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-03-17 01:01:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:01:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:01:33] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-03-17 01:01:33] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-03-17 01:01:33] [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.
[2025-03-17 01:01:33] [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
[2025-03-17 01:01:33] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-03-17 01:01:33] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-03-17 01:01:33] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-03-17 01:01:33] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-03-17 01:01:33] [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`.
[2025-03-17 01:01:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-03-17 01:01:33] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): loaded 20417 records from cache
[2025-03-17 01:01:34] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’
--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:01:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-17 01:01:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:01:53] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
--- finished re-building ‘drug_targets.Rmd’
--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2025-03-17 01:02:05] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:02:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-03-17 01:02:05] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:02:05] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:02:05] [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`
[2025-03-17 01:02:05] [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`
[2025-03-17 01:02:05] [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`
[2025-03-17 01:02:05] [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`
[2025-03-17 01:02:05] [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`
[2025-03-17 01:02:05] [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`
[2025-03-17 01:02:05] [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`
[2025-03-17 01:02:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:02:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:02:09] [TRACE] [OmnipathR] Downloaded 3.5 Mb in 3.498236s from omnipathdb.org (1021.1 Kb/s); Redirect: 0s, DNS look up: 0.004287s, Connection: 0.170819s, Pretransfer: 0.340772s, First byte at: 0.67432s
[2025-03-17 01:02:10] [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`
[2025-03-17 01:02:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:02:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:02:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:02:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:02:10] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:02:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-03-17 01:02:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-03-17 01:02:11] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-03-17 01:02:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:02:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:02:11] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-03-17 01:02:11] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-17 01:02:29] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-03-17 01:14:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:14:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-03-17 01:14:04] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:14:04] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:14:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:14:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:14:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:14:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:14:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:14:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:14:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:14:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:14:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:14:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:16:59] [TRACE] [OmnipathR] Downloaded 1.9 Mb in 2m 53.199409s from omnipathdb.org (11 Kb/s); Redirect: 0s, DNS look up: 0.006636s, Connection: 0.174441s, Pretransfer: 0.345683s, First byte at: 0.850422s
[2025-03-17 01:16:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-03-17 01:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:16:59] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:17:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-03-17 01:17:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-03-17 01:17:00] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-03-17 01:17:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:17:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:00] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-03-17 01:17:00] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-17 01:17:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-17 01:17:01] [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`
[2025-03-17 01:17:01] [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`
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-17 01:17:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-17 01:17:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:17:01] [TRACE] [OmnipathR] Downloaded 5.1 Kb in 0.502467s from omnipathdb.org (10.1 Kb/s); Redirect: 0s, DNS look up: 0.000864s, Connection: 0.167085s, Pretransfer: 0.33676s, First byte at: 0.502428s
[2025-03-17 01:17:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-03-17 01:17:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:17:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:17:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:02] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:17:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-03-17 01:17:02] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-03-17 01:17:02] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-03-17 01:17:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:17:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:02] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-03-17 01:17:02] [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
[2025-03-17 01:17:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:17:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-03-17 01:17:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:17:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-03-17 01:17:07] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:17:07] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:17:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:17:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:08] [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`
[2025-03-17 01:17:08] [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`
[2025-03-17 01:17:08] [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`
[2025-03-17 01:17:08] [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`
[2025-03-17 01:17:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:08] [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`
[2025-03-17 01:17:08] [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`
[2025-03-17 01:17:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:17:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:17:27] [TRACE] [OmnipathR] Downloaded 1.6 Mb in 19.101187s from omnipathdb.org (85.1 Kb/s); Redirect: 0s, DNS look up: 0.000866s, Connection: 0.167982s, Pretransfer: 0.339209s, First byte at: 0.843508s
[2025-03-17 01:17:28] [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`
[2025-03-17 01:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:28] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:17:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-03-17 01:17:29] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-03-17 01:17:29] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-03-17 01:17:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:17:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:29] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-03-17 01:17:32] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-03-17 01:17:41] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:17:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-03-17 01:17:41] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:17:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-03-17 01:17:41] [TRACE] [OmnipathR] Organism(s): 10090
[2025-03-17 01:17:41] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:17:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:17:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:17:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:17:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:17:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:18:02] [TRACE] [OmnipathR] Downloaded 1.2 Mb in 19.372497s from omnipathdb.org (64.3 Kb/s); Redirect: 0s, DNS look up: 0.000798s, Connection: 0.167263s, Pretransfer: 0.337019s, First byte at: 0.668834s
[2025-03-17 01:18:02] [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`
[2025-03-17 01:18:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:02] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:18:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-03-17 01:18:03] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-03-17 01:18:03] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-03-17 01:18:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:03] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-03-17 01:18:06] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-03-17 01:18:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-03-17 01:18:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-03-17 01:18:06] [TRACE] [OmnipathR] Organism(s): 10116
[2025-03-17 01:18:06] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:18:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:17] [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`
[2025-03-17 01:18:17] [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`
[2025-03-17 01:18:17] [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`
[2025-03-17 01:18:17] [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`
[2025-03-17 01:18:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:17] [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`
[2025-03-17 01:18:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:18:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:18:19] [TRACE] [OmnipathR] Downloaded 438.4 Kb in 1.3329s from omnipathdb.org (328.9 Kb/s); Redirect: 0s, DNS look up: 0.00074s, Connection: 0.167271s, Pretransfer: 0.337248s, First byte at: 0.669488s
[2025-03-17 01:18:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:20] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-03-17 01:18:20] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:20] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-03-17 01:18:20] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:18:20] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:18:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:21] [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`
[2025-03-17 01:18:21] [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`
[2025-03-17 01:18:21] [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`
[2025-03-17 01:18:21] [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`
[2025-03-17 01:18:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:21] [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`
[2025-03-17 01:18:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:18:21] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:18:34] [TRACE] [OmnipathR] Downloaded 188.5 Kb in 12.371224s from omnipathdb.org (15.2 Kb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 1.174099s, Pretransfer: 1.508837s, First byte at: 2.637544s
[2025-03-17 01:18:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:35] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-03-17 01:18:35] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:35] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-03-17 01:18:35] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-17 01:18:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:40] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-17 01:18:42] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-03-17 01:18:42] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:18:42] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:42] [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`
[2025-03-17 01:18:42] [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`
[2025-03-17 01:18:42] [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`
[2025-03-17 01:18:42] [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`
[2025-03-17 01:18:42] [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`
[2025-03-17 01:18:42] [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`
[2025-03-17 01:18:42] [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`
[2025-03-17 01:18:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:18:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:18:43] [TRACE] [OmnipathR] Downloaded 264.9 Kb in 1.169048s from omnipathdb.org (226.6 Kb/s); Redirect: 0s, DNS look up: 0.000762s, Connection: 0.166676s, Pretransfer: 0.337256s, First byte at: 0.669674s
[2025-03-17 01:18:45] [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`
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:45] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-03-17 01:18:45] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:45] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-03-17 01:18:45] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:18:45] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:18:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:47] [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`
[2025-03-17 01:18:47] [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`
[2025-03-17 01:18:47] [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`
[2025-03-17 01:18:47] [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`
[2025-03-17 01:18:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:47] [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`
[2025-03-17 01:18:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:18:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:18:48] [TRACE] [OmnipathR] Downloaded 25.1 Kb in 0.678087s from omnipathdb.org (37 Kb/s); Redirect: 0s, DNS look up: 0.000862s, Connection: 0.167852s, Pretransfer: 0.339004s, First byte at: 0.672216s
[2025-03-17 01:18:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:49] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:18:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-03-17 01:18:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-03-17 01:18:49] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-03-17 01:18:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:49] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-03-17 01:18:49] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2025-03-17 01:18:50] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-03-17 01:18:50] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:18:50] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:50] [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`
[2025-03-17 01:18:50] [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`
[2025-03-17 01:18:50] [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`
[2025-03-17 01:18:50] [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`
[2025-03-17 01:18:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-03-17 01:18:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-03-17 01:18:50] [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`
[2025-03-17 01:18:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:18:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:18:50] [TRACE] [OmnipathR] Downloaded 2.2 Kb in 0.507842s from omnipathdb.org (4.2 Kb/s); Redirect: 0s, DNS look up: 0.000747s, Connection: 0.168303s, Pretransfer: 0.340031s, First byte at: 0.507812s
[2025-03-17 01:18:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-03-17 01:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:51] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:18:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-03-17 01:18:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-03-17 01:18:51] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-03-17 01:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:51] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-03-17 01:18:51] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2025-03-17 01:18:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:18:54] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-03-17 01:18:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:18:54] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-03-17 01:18:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:57] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache.
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:18:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-17 01:18:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:19:02] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-03-17 01:19:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:19:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2025-03-17 01:19:04] [TRACE] [OmnipathR] Organism(s): 10090
[2025-03-17 01:19:04] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:19:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:19:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:19:05] [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`
[2025-03-17 01:19:05] [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`
[2025-03-17 01:19:05] [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`
[2025-03-17 01:19:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:19:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:19:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:19:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:19:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:19:30] [TRACE] [OmnipathR] Downloaded 446.1 Kb in 24.666514s from omnipathdb.org (18.1 Kb/s); Redirect: 0s, DNS look up: 0.00078s, Connection: 0.16683s, Pretransfer: 0.337389s, First byte at: 0.836504s
[2025-03-17 01:19:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-03-17 01:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:31] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:19:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-03-17 01:19:31] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-03-17 01:19:31] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2025-03-17 01:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:31] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2025-03-17 01:19:32] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2025-03-17 01:19:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:19:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:33] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:19:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-03-17 01:19:33] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:19:33] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:19:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:40] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:40] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:19:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:19:50] [TRACE] [OmnipathR] Downloaded 279.5 Kb in 10.603432s from omnipathdb.org (26.4 Kb/s); Redirect: 0s, DNS look up: 0.000721s, Connection: 0.167579s, Pretransfer: 0.338589s, First byte at: 0.840295s
[2025-03-17 01:19:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-03-17 01:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:51] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:19:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-03-17 01:19:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-03-17 01:19:51] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2025-03-17 01:19:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:19:51] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2025-03-17 01:19:51] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2025-03-17 01:20:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:20:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:41] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:20:41] [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]
[2025-03-17 01:20:41] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:20:41] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:20:41] [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`
[2025-03-17 01:20:41] [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`
[2025-03-17 01:20:41] [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`
[2025-03-17 01:20:41] [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`
[2025-03-17 01:20:41] [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`
[2025-03-17 01:20:41] [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`
[2025-03-17 01:20:41] [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`
[2025-03-17 01:20:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:20:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:20:45] [TRACE] [OmnipathR] Downloaded 15 Kb in 3.744959s from omnipathdb.org (4 Kb/s); Redirect: 0s, DNS look up: 0.000823s, Connection: 2.194782s, Pretransfer: 2.747409s, First byte at: 3.744261s
[2025-03-17 01:20:46] [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`
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:46] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-03-17 01:20:46] [INFO] [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1]
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:46] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`.
[2025-03-17 01:20:46] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records.
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:20:46] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:20:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:20:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:55] [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`
[2025-03-17 01:20:55] [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`
[2025-03-17 01:20:55] [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`
[2025-03-17 01:20:55] [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`
[2025-03-17 01:20:55] [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`
[2025-03-17 01:20:55] [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`
[2025-03-17 01:20:55] [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`
[2025-03-17 01:20:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:20:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:20:58] [TRACE] [OmnipathR] Downloaded 5.8 Kb in 2.928438s from omnipathdb.org (2 Kb/s); Redirect: 0s, DNS look up: 0.000706s, Connection: 2.204709s, Pretransfer: 2.542858s, First byte at: 2.928404s
[2025-03-17 01:20:59] [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`
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:20:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:20:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:59] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-03-17 01:20:59] [INFO] [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1]
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:20:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:20:59] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`.
[2025-03-17 01:20:59] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:20:59] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:21:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:21:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:21:01] [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`
[2025-03-17 01:21:01] [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`
[2025-03-17 01:21:01] [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`
[2025-03-17 01:21:01] [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`
[2025-03-17 01:21:01] [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`
[2025-03-17 01:21:01] [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`
[2025-03-17 01:21:01] [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`
[2025-03-17 01:21:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:21:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:21:03] [TRACE] [OmnipathR] Downloaded 3.8 Kb in 1.845564s from omnipathdb.org (2 Kb/s); Redirect: 0s, DNS look up: 0.000765s, Connection: 0.168161s, Pretransfer: 1.019246s, First byte at: 1.845394s
[2025-03-17 01:21:04] [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`
[2025-03-17 01:21:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:21:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:21:04] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:21:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-03-17 01:21:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-03-17 01:21:04] [INFO] [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1]
[2025-03-17 01:21:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:21:04] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`.
[2025-03-17 01:21:04] [SUCCESS] [OmnipathR] Downloaded 424 annotation records.
[2025-03-17 01:21:05] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:21:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-03-17 01:21:05] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:21:05] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:21:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-03-17 01:21:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-03-17 01:21:13] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-03-17 01:21:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2025-03-17 01:21:13] [SUCCESS] [OmnipathR] Loaded 1098 records from cache.
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:21:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:21:35] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` (attempt 1/3); error: Failure when receiving data from the peer [omnipathdb.org]: Recv failure: Connection reset by peer
[2025-03-17 01:21:40] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:21:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:21:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:22:15] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` (attempt 2/3); error: Failure when receiving data from the peer [omnipathdb.org]: Recv failure: Connection reset by peer
[2025-03-17 01:22:20] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:22:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:22:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:24:52] [TRACE] [OmnipathR] Downloaded 4.7 Mb in 2m 30.671491s from omnipathdb.org (32.3 Kb/s); Redirect: 0s, DNS look up: 0.000676s, Connection: 0.167807s, Pretransfer: 0.33951s, First byte at: 0.678595s
[2025-03-17 01:24:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-03-17 01:24:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:24:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:24:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:24:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:24:53] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:24:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-03-17 01:24:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-03-17 01:24:54] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2025-03-17 01:24:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:24:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:24:54] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2025-03-17 01:24:55] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2025-03-17 01:24:55] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-03-17 01:24:55] [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.
[2025-03-17 01:24:55] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2025-03-17 01:24:55] [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
[2025-03-17 01:24:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:24:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-03-17 01:24:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:24:57] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:25:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:25:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:25:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:25:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:25:02] [TRACE] [OmnipathR] Downloaded 29.2 Kb in 0.673348s from omnipathdb.org (43.3 Kb/s); Redirect: 0s, DNS look up: 0.000756s, Connection: 0.166797s, Pretransfer: 0.336494s, First byte at: 0.669069s
[2025-03-17 01:25:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-03-17 01:25:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:25:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:25:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:25:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:25:03] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:25:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-03-17 01:25:03] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-03-17 01:25:03] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-03-17 01:25:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:25:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:25:03] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-03-17 01:25:03] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-03-17 01:25:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-03-17 01:25:04] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-03-17 01:25:04] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-03-17 01:25:04] [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`.
[2025-03-17 01:25:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:25:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:25:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:25:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:25:04] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:25:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-03-17 01:25:04] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-03-17 01:25:04] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-03-17 01:25:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:25:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:25:06] [TRACE] [OmnipathR] Downloaded 157.2 Kb in 2.092038s from static-content.springer.com (75.1 Kb/s); Redirect: 0s, DNS look up: 0.012029s, Connection: 0.013946s, Pretransfer: 0.040454s, First byte at: 2.074209s
[2025-03-17 01:25:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-03-17 01:25:07] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-03-17 01:25:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:25:07] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-03-17 01:25:07] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-03-17 01:25:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:25:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-03-17 01:25:07] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:25:07] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:25:07] [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`
[2025-03-17 01:25:07] [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`
[2025-03-17 01:25:07] [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`
[2025-03-17 01:25:07] [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`
[2025-03-17 01:25:07] [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`
[2025-03-17 01:25:07] [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`
[2025-03-17 01:25:07] [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`
[2025-03-17 01:25:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:25:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:02] [TRACE] [OmnipathR] Downloaded 2.1 Mb in 54.626649s from omnipathdb.org (38.5 Kb/s); Redirect: 0s, DNS look up: 0.000773s, Connection: 0.166323s, Pretransfer: 1.00842s, First byte at: 1.511948s
[2025-03-17 01:26:03] [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`
[2025-03-17 01:26:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:03] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-03-17 01:26:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-03-17 01:26:04] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-03-17 01:26:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:04] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:10] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-03-17 01:26:10] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:26:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-03-17 01:26:10] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:10] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-17 01:26:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-17 01:26:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-17 01:26:11] [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`
[2025-03-17 01:26:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-17 01:26:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-17 01:26:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-17 01:26:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:14] [TRACE] [OmnipathR] Downloaded 2.4 Mb in 2.576133s from omnipathdb.org (958.3 Kb/s); Redirect: 0s, DNS look up: 0.00068s, Connection: 0.168221s, Pretransfer: 0.339282s, First byte at: 0.676964s
[2025-03-17 01:26:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-03-17 01:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:15] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-03-17 01:26:16] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-03-17 01:26:16] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-03-17 01:26:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:16] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:16] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-03-17 01:26:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:17] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:18] [TRACE] [OmnipathR] Downloaded 110.8 Kb in 1.014941s from omnipathdb.org (109.1 Kb/s); Redirect: 0s, DNS look up: 0.000789s, Connection: 0.169144s, Pretransfer: 0.341333s, First byte at: 0.67831s
[2025-03-17 01:26:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:19] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-03-17 01:26:19] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:19] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:19] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:19] [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`
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:21] [TRACE] [OmnipathR] Downloaded 310.9 Kb in 1.170231s from omnipathdb.org (265.7 Kb/s); Redirect: 0s, DNS look up: 0.000741s, Connection: 0.166501s, Pretransfer: 0.33626s, First byte at: 0.667959s
[2025-03-17 01:26:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:22] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-17 01:26:22] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:22] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:22] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:23] [TRACE] [OmnipathR] Downloaded 251.9 Kb in 1.178569s from omnipathdb.org (213.7 Kb/s); Redirect: 0s, DNS look up: 0.000736s, Connection: 0.166997s, Pretransfer: 0.342605s, First byte at: 0.678929s
[2025-03-17 01:26:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-03-17 01:26:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:24] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-03-17 01:26:24] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-03-17 01:26:24] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-03-17 01:26:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:24] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:24] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-17 01:26:25] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:25] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:25] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:26] [TRACE] [OmnipathR] Downloaded 157.9 Kb in 1.008576s from omnipathdb.org (156.5 Kb/s); Redirect: 0s, DNS look up: 0.000734s, Connection: 0.169542s, Pretransfer: 0.339381s, First byte at: 0.670926s
[2025-03-17 01:26:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:27] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-03-17 01:26:27] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:27] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:27] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-17 01:26:27] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:27] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:29] [TRACE] [OmnipathR] Downloaded 306.2 Kb in 1.177442s from omnipathdb.org (260.1 Kb/s); Redirect: 0s, DNS look up: 0.000763s, Connection: 0.167505s, Pretransfer: 0.338634s, First byte at: 0.672216s
[2025-03-17 01:26:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-03-17 01:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:30] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-03-17 01:26:30] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:30] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:30] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-03-17 01:26:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-03-17 01:26:30] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:30] [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`
[2025-03-17 01:26:30] [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`
[2025-03-17 01:26:30] [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`
[2025-03-17 01:26:30] [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`
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-03-17 01:26:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-03-17 01:26:30] [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`
[2025-03-17 01:26:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:48] [TRACE] [OmnipathR] Downloaded 1.5 Mb in 17.288699s from omnipathdb.org (88.7 Kb/s); Redirect: 0s, DNS look up: 0.000719s, Connection: 0.169346s, Pretransfer: 0.341579s, First byte at: 0.678163s
[2025-03-17 01:26:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-03-17 01:26:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:49] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-03-17 01:26:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-03-17 01:26:50] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-03-17 01:26:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:50] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:52] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-03-17 01:26:52] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:26:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-03-17 01:26:52] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:52] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:26:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:54] [TRACE] [OmnipathR] Downloaded 13.1 Kb in 0.669287s from omnipathdb.org (19.6 Kb/s); Redirect: 0s, DNS look up: 0.000954s, Connection: 0.166839s, Pretransfer: 0.337238s, First byte at: 0.668964s
[2025-03-17 01:26:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:55] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-03-17 01:26:55] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:55] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:55] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:55] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:26:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:26:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:26:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:26:57] [TRACE] [OmnipathR] Downloaded 12.1 Kb in 0.674802s from omnipathdb.org (17.9 Kb/s); Redirect: 0s, DNS look up: 0.00079s, Connection: 0.167767s, Pretransfer: 0.340349s, First byte at: 0.674482s
[2025-03-17 01:26:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-03-17 01:26:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:58] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:26:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-03-17 01:26:58] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-03-17 01:26:58] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-03-17 01:26:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:26:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:26:58] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-03-17 01:26:58] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-03-17 01:26:59] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-03-17 01:26:59] [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.
[2025-03-17 01:26:59] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:26:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-03-17 01:26:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:26:59] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:27:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:27:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:00] [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`
[2025-03-17 01:27:00] [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`
[2025-03-17 01:27:00] [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`
[2025-03-17 01:27:00] [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`
[2025-03-17 01:27:00] [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`
[2025-03-17 01:27:00] [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`
[2025-03-17 01:27:00] [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`
[2025-03-17 01:27:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:27:00] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:27:01] [TRACE] [OmnipathR] Downloaded 11.7 Kb in 0.50873s from omnipathdb.org (23 Kb/s); Redirect: 0s, DNS look up: 0.000859s, Connection: 0.167817s, Pretransfer: 0.338671s, First byte at: 0.508443s
[2025-03-17 01:27:02] [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`
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:27:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:27:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:02] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-03-17 01:27:02] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:27:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:02] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-03-17 01:27:02] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:27:02] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:27:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:27:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:27:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-17 01:27:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:27:03] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-03-17 01:27:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:27:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-03-17 01:27:04] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:27:04] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:27:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:27:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-17 01:27:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-03-17 01:27:06] [TRACE] [OmnipathR] Downloaded 20.2 Kb in 0.674973s from omnipathdb.org (29.9 Kb/s); Redirect: 0s, DNS look up: 0.000736s, Connection: 0.166888s, Pretransfer: 0.337198s, First byte at: 0.669878s
[2025-03-17 01:27:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:27:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:27:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:07] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-03-17 01:27:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-03-17 01:27:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-03-17 01:27:07] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-03-17 01:27:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 01:27:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:07] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-03-17 01:27:07] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-03-17 01:27:11] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:27:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-03-17 01:27:11] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:27:11] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:27:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:27:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:27:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-03-17 01:27:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-03-17 01:27:12] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-03-17 01:27:12] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-03-17 01:27:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-03-17 01:27:12] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-17 01:27:12] [TRACE] [OmnipathR] Orthology targets:
[2025-03-17 01:27:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-17 01:27:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-17 01:27:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-03-17 01:27:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-03-17 01:27:13] [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