[ Started: 2025-03-14 00:18:07 CET ]
[ OmnipathR v3.15.11 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (7c69da1 2025-02-25 22:51:58) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-02-12 r87715)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.11’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) 
See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-13 23:17:02 UTC; omnipath
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 23:18:10 UTC; unix
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-14; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-14 00:18:36] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-14 00:18:36] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); 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); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); 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(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); 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); 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 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-14 00:18:36] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:36] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
ungroup:
  function(x, ...)
ungroup.tbl_attrs:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-13 23:17:02 UTC; omnipath
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 23:18:10 UTC; unix
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-03-14; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-14 00:18:46] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-14 00:18:46] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); 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); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); 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(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); 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); 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 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-14 00:18:46] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:18:46] [TRACE]   [OmnipathR] Cache locked: FALSE
ambiguity_summarize: no visible binding for global variable ‘data’
download_base : fun: no visible global function definition for
  ‘headers’
download_base : fun: no visible binding for global variable ‘response’
inbiomap_cookie: no visible binding for global variable ‘init_post’
inbiomap_cookie: no visible binding for global variable ‘post’
inbiomap_cookie: no visible binding for global variable ‘init_payload’
inbiomap_cookie: no visible binding for global variable ‘payload’
inbiomap_cookie: no visible binding for global variable ‘curl_verbose’
log_packages: no visible binding for global variable ‘package’
log_packages: no visible binding for global variable ‘loadedversion’
log_welcome: no visible binding for global variable ‘pkgname’
translate_ids : <anonymous>: no visible binding for global variable
  ‘From’
xls_downloader: possible error in download_to_cache(url_key = url_key,
  url_key_param = url_key_param, url_param = url_param, ext = ext,
  http_param = http_param, post = post): unused argument (http_param =
  http_param)
Undefined global functions or variables:
  From curl_verbose data headers init_payload init_post loadedversion
  package payload pkgname post response
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'ambiguity.Rd'
  ‘from_col’ ‘to_col’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' import not declared from: ‘httr’
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: curated_ligrec_stats
> ### Title: Statistics about literature curated ligand-receptor interactions
> ### Aliases: curated_ligrec_stats
> 
> ### ** Examples
> 
> clr <- curated_ligrec_stats()
Warning in import_post_translational_interactions(resources = ., ...) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions]
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2025-03-14 00:20:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:48] [SUCCESS] [OmnipathR] Loaded 4568 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2025-03-14 00:20:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:20:48] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2025-03-14 00:20:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:48] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:20:48] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2025-03-14 00:20:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:20:49] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2025-03-14 00:20:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:20:50] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2025-03-14 00:20:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:50] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations]
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2025-03-14 00:20:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-14 00:20:50] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:20:51] [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=1,ssl_verifyhost=2]
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Downloaded 110.7 Kb in 0.563291s from omnipathdb.org (196.6 Kb/s); Redirect: 0s, DNS look up: 0.001014s, Connection: 0.016884s, Pretransfer: 0.050807s, First byte at: 0.531479s
[2025-03-14 00:20:51] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:51] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-03-14 00:20:51] [INFO]    [OmnipathR] Download ready [key=afe18d85fba82fa7d5f390113de328e13aa85e89, version=1]
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:51] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `started` to `ready`.
[2025-03-14 00:20:51] [SUCCESS] [OmnipathR] Downloaded 2879 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:51] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-03-14 00:20:52] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:52] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-03-14 00:20:52] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:52] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2025-03-14 00:20:52] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:52] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:20:53] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions]
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:53] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:20:53] [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=1,ssl_verifyhost=2]
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Downloaded 189.5 Kb in 0.72355s from omnipathdb.org (261.9 Kb/s); Redirect: 0s, DNS look up: 0.000874s, Connection: 0.018839s, Pretransfer: 0.063176s, First byte at: 0.652092s
[2025-03-14 00:20:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:54] [INFO]    [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-03-14 00:20:54] [INFO]    [OmnipathR] Download ready [key=c8350370602bcfe8ed14bda96cb9bd68770c1e66, version=1]
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:54] [INFO]    [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `started` to `ready`.
[2025-03-14 00:20:54] [SUCCESS] [OmnipathR] Downloaded 3765 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions]
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-03-14 00:20:54] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:54] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions]
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:54] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2025-03-14 00:20:54] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2025-03-14 00:20:55] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:20:55] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:20:55] [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=1,ssl_verifyhost=2]
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Downloaded 203.1 Kb in 0.699271s from omnipathdb.org (290.4 Kb/s); Redirect: 0s, DNS look up: 0.001068s, Connection: 0.019076s, Pretransfer: 0.05238s, First byte at: 0.626194s
[2025-03-14 00:20:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:56] [INFO]    [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-03-14 00:20:56] [INFO]    [OmnipathR] Download ready [key=8158e608d1fd5182b9aa0a24a07fc739c59a1bf8, version=1]
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:56] [INFO]    [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `started` to `ready`.
[2025-03-14 00:20:56] [SUCCESS] [OmnipathR] Downloaded 3473 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:56] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-03-14 00:20:57] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:57] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-03-14 00:20:57] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:57] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions]
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2025-03-14 00:20:57] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:57] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions]
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:20:58] [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=1,ssl_verifyhost=2]
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Downloaded 94.9 Kb in 0.577522s from omnipathdb.org (164.3 Kb/s); Redirect: 0s, DNS look up: 0.000942s, Connection: 0.018254s, Pretransfer: 0.053438s, First byte at: 0.542306s
[2025-03-14 00:20:58] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:58] [INFO]    [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-03-14 00:20:58] [INFO]    [OmnipathR] Download ready [key=641434253ee9e555515168e62fe5c7e36a8596c6, version=1]
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:20:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:58] [INFO]    [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `started` to `ready`.
[2025-03-14 00:20:59] [SUCCESS] [OmnipathR] Downloaded 1894 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions]
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-03-14 00:20:59] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:59] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions]
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2025-03-14 00:20:59] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:20:59] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2025-03-14 00:20:59] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:20:59] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:20:59] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:00] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Downloaded 77.9 Kb in 0.431524s from omnipathdb.org (180.5 Kb/s); Redirect: 0s, DNS look up: 0.000899s, Connection: 0.01682s, Pretransfer: 0.061334s, First byte at: 0.41453s
[2025-03-14 00:21:00] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:00] [INFO]    [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-03-14 00:21:00] [INFO]    [OmnipathR] Download ready [key=af0debe0cdd22707b097cd388dfd1398cccb76c8, version=1]
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:00] [INFO]    [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:00] [SUCCESS] [OmnipathR] Downloaded 1000 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-03-14 00:21:01] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-03-14 00:21:01] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions]
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2025-03-14 00:21:01] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:01] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] Downloaded 175.8 Kb in 0.797355s from omnipathdb.org (220.5 Kb/s); Redirect: 0s, DNS look up: 0.000987s, Connection: 0.02068s, Pretransfer: 0.069283s, First byte at: 0.719706s
[2025-03-14 00:21:02] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:02] [INFO]    [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-03-14 00:21:02] [INFO]    [OmnipathR] Download ready [key=d08eb76734c005daabb6eb3c832a55e330672026, version=1]
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:02] [INFO]    [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:03] [SUCCESS] [OmnipathR] Downloaded 2313 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-03-14 00:21:03] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:03] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-03-14 00:21:03] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:03] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions]
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:03] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2025-03-14 00:21:03] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:04] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:04] [TRACE]   [OmnipathR] Downloaded 69.1 Kb in 0.512417s from omnipathdb.org (134.9 Kb/s); Redirect: 0s, DNS look up: 0.000861s, Connection: 0.020466s, Pretransfer: 0.064648s, First byte at: 0.492609s
[2025-03-14 00:21:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:05] [INFO]    [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-03-14 00:21:05] [INFO]    [OmnipathR] Download ready [key=11b0dd49c2e8541d966f577a8aacd52c71112987, version=1]
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:05] [INFO]    [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:05] [SUCCESS] [OmnipathR] Downloaded 672 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-03-14 00:21:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:05] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-03-14 00:21:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:05] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions]
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2025-03-14 00:21:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:05] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:06] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Downloaded 132.3 Kb in 0.659904s from omnipathdb.org (200.4 Kb/s); Redirect: 0s, DNS look up: 0.001039s, Connection: 0.020973s, Pretransfer: 0.070113s, First byte at: 0.599745s
[2025-03-14 00:21:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:06] [INFO]    [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-03-14 00:21:06] [INFO]    [OmnipathR] Download ready [key=f963006a054fdbb2fcbd5a63e731087e21fb4b31, version=1]
[2025-03-14 00:21:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:07] [INFO]    [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:07] [SUCCESS] [OmnipathR] Downloaded 1676 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-03-14 00:21:07] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:07] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-03-14 00:21:07] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:07] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions]
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2025-03-14 00:21:07] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:07] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-03-14 00:21:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:08] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Downloaded 20.8 Kb in 0.412545s from omnipathdb.org (50.4 Kb/s); Redirect: 0s, DNS look up: 0.001074s, Connection: 0.020378s, Pretransfer: 0.05533s, First byte at: 0.411365s
[2025-03-14 00:21:08] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:08] [INFO]    [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-03-14 00:21:08] [INFO]    [OmnipathR] Download ready [key=e59c495f650b38ab64da89e0da5af6ff096901b8, version=1]
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:08] [INFO]    [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:08] [SUCCESS] [OmnipathR] Downloaded 152 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-03-14 00:21:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-03-14 00:21:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions]
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2025-03-14 00:21:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:09] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Downloaded 160.9 Kb in 0.710254s from omnipathdb.org (226.6 Kb/s); Redirect: 0s, DNS look up: 0.001102s, Connection: 0.019894s, Pretransfer: 0.053259s, First byte at: 0.634775s
[2025-03-14 00:21:10] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:10] [INFO]    [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-03-14 00:21:10] [INFO]    [OmnipathR] Download ready [key=78bff68f8413d6211070111914db1b8b2b98ad54, version=1]
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:10] [INFO]    [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:10] [SUCCESS] [OmnipathR] Downloaded 1946 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-03-14 00:21:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:11] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-03-14 00:21:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:11] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions]
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2025-03-14 00:21:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:11] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:12] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Downloaded 57.6 Kb in 0.483713s from omnipathdb.org (119 Kb/s); Redirect: 0s, DNS look up: 0.001112s, Connection: 0.021116s, Pretransfer: 0.054106s, First byte at: 0.46365s
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Download ready [key=4d3e24d35f89a47701b9f0e9d5da90ec2aee0874, version=1]
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:12] [SUCCESS] [OmnipathR] Downloaded 479 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-03-14 00:21:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-03-14 00:21:13] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions]
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2025-03-14 00:21:13] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions]
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:13] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Downloaded 175 Kb in 0.748976s from omnipathdb.org (233.6 Kb/s); Redirect: 0s, DNS look up: 0.000986s, Connection: 0.018197s, Pretransfer: 0.051505s, First byte at: 0.680404s
[2025-03-14 00:21:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:14] [INFO]    [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-03-14 00:21:14] [INFO]    [OmnipathR] Download ready [key=2fed349a0caf2a5e7555cbd27caa66d55fd06302, version=1]
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:14] [INFO]    [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:14] [SUCCESS] [OmnipathR] Downloaded 2484 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions]
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-03-14 00:21:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:15] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions]
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2025-03-14 00:21:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:15] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions]
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2025-03-14 00:21:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-03-14 00:21:15] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-03-14 00:21:15] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:16] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Downloaded 67.3 Kb in 0.502939s from omnipathdb.org (133.9 Kb/s); Redirect: 0s, DNS look up: 0.000912s, Connection: 0.020179s, Pretransfer: 0.054236s, First byte at: 0.483371s
[2025-03-14 00:21:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:17] [INFO]    [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-03-14 00:21:17] [INFO]    [OmnipathR] Download ready [key=d78f1e5d23782453249e01fb0379efde9c053131, version=1]
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:17] [INFO]    [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:17] [SUCCESS] [OmnipathR] Downloaded 1018 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-03-14 00:21:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:17] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-03-14 00:21:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:17] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions]
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2025-03-14 00:21:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:18] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:18] [TRACE]   [OmnipathR] Downloaded 117.4 Kb in 0.577658s from omnipathdb.org (203.2 Kb/s); Redirect: 0s, DNS look up: 0.000928s, Connection: 0.016225s, Pretransfer: 0.050796s, First byte at: 0.544722s
[2025-03-14 00:21:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:19] [INFO]    [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-03-14 00:21:19] [INFO]    [OmnipathR] Download ready [key=ef7eb533b45a8e6a8f4b6e928698c193d947a86b, version=1]
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:19] [INFO]    [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:19] [SUCCESS] [OmnipathR] Downloaded 1707 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-03-14 00:21:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:19] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-03-14 00:21:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:19] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions]
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2025-03-14 00:21:20] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:20] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Downloaded 197 Kb in 0.771184s from omnipathdb.org (255.5 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.020029s, Pretransfer: 0.05369s, First byte at: 0.694666s
[2025-03-14 00:21:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:21] [INFO]    [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-03-14 00:21:21] [INFO]    [OmnipathR] Download ready [key=0ae240e6276d9da6cd5c362b0e477962ece2e997, version=1]
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:21] [INFO]    [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:21] [SUCCESS] [OmnipathR] Downloaded 3310 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-03-14 00:21:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:21] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:21] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-03-14 00:21:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions]
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2025-03-14 00:21:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:22] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Downloaded 181.4 Kb in 0.707184s from omnipathdb.org (256.5 Kb/s); Redirect: 0s, DNS look up: 0.001103s, Connection: 0.019023s, Pretransfer: 0.067137s, First byte at: 0.635972s
[2025-03-14 00:21:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:23] [INFO]    [OmnipathR] Cache item `b5d1617be0762d096dbf001209e826bff4794c4d` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-03-14 00:21:23] [INFO]    [OmnipathR] Download ready [key=b5d1617be0762d096dbf001209e826bff4794c4d, version=1]
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:23] [INFO]    [OmnipathR] Cache item `b5d1617be0762d096dbf001209e826bff4794c4d` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:23] [SUCCESS] [OmnipathR] Downloaded 2639 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:23] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-03-14 00:21:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:24] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-03-14 00:21:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:24] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=iTALK,query_type=interactions]
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2025-03-14 00:21:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:24] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:24] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:25] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Downloaded 172.1 Kb in 0.605522s from omnipathdb.org (284.2 Kb/s); Redirect: 0s, DNS look up: 0.000919s, Connection: 0.020453s, Pretransfer: 0.053644s, First byte at: 0.526394s
[2025-03-14 00:21:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:25] [INFO]    [OmnipathR] Cache item `1865fc4065462281aedd5a4132fdb7bda8fbb889` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2025-03-14 00:21:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2025-03-14 00:21:26] [INFO]    [OmnipathR] Download ready [key=1865fc4065462281aedd5a4132fdb7bda8fbb889, version=1]
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:26] [INFO]    [OmnipathR] Cache item `1865fc4065462281aedd5a4132fdb7bda8fbb889` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:26] [SUCCESS] [OmnipathR] Downloaded 1796 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2025-03-14 00:21:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:26] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2025-03-14 00:21:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:26] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2025-03-14 00:21:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:26] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations]
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2025-03-14 00:21:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-03-14 00:21:27] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=HPMR,query_type=interactions]
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-14 00:21:27] [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=1,ssl_verifyhost=2]
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Downloaded 54.4 Kb in 0.373315s from omnipathdb.org (145.8 Kb/s); Redirect: 0s, DNS look up: 0.001033s, Connection: 0.020108s, Pretransfer: 0.053368s, First byte at: 0.352933s
[2025-03-14 00:21:27] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPMR&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:28] [INFO]    [OmnipathR] Cache item `b01662e96d972605030897d8cbd9f5efafd68f89` version 1: status changed from `unknown` to `started`.
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b01662e96d972605030897d8cbd9f5efafd68f89-1.rds`.
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b01662e96d972605030897d8cbd9f5efafd68f89-1.rds`.
[2025-03-14 00:21:28] [INFO]    [OmnipathR] Download ready [key=b01662e96d972605030897d8cbd9f5efafd68f89, version=1]
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 00:21:28] [INFO]    [OmnipathR] Cache item `b01662e96d972605030897d8cbd9f5efafd68f89` version 1: status changed from `started` to `ready`.
[2025-03-14 00:21:28] [SUCCESS] [OmnipathR] Downloaded 461 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=HPMR,query_type=interactions]
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-14 00:21:28] [TRACE]   [OmnipathR] Orthology targets: 
Error in `map()`:
ℹ In index: 18.
Caused by error in `map()`:
ℹ In index: 2.
Caused by error in `file()`:
! cannot open the connection to 'https://omnipathdb.org/resources'
Backtrace:
     ▆
  1. ├─OmnipathR::curated_ligrec_stats()
  2. │ └─... %>% unnest_wider(col = data)
  3. ├─OmnipathR:::unnest_wider(., col = data)
  4. │ └─base::eval(call[[tbl_name]], parent.frame())
  5. │   └─base::eval(call[[tbl_name]], parent.frame())
  6. ├─tibble::tibble(resource = names(.), data = .)
  7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
  8. │   └─rlang::eval_tidy(xs[[j]], mask)
  9. ├─rlang::set_names(map(., stats_one_resource, curated), .)
 10. ├─purrr::map(., stats_one_resource, curated)
 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 12. │   ├─purrr:::with_indexed_errors(...)
 13. │   │ └─base::withCallingHandlers(...)
 14. │   ├─purrr:::call_with_cleanup(...)
 15. │   └─OmnipathR (local) .f(.x[[i]], ...)
 16. │     └─... %>% ...
 17. ├─purrr::map(., nrow)
 18. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 19. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
 20. ├─rlang::set_names(...)
 21. ├─purrr::map(...)
 22. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 23. │   ├─purrr:::with_indexed_errors(...)
 24. │   │ └─base::withCallingHandlers(...)
 25. │   ├─purrr:::call_with_cleanup(...)
 26. │   └─OmnipathR (local) .f(.x[[i]], ...)
 27. │     └─get(sprintf("%s_one_resource", field))(resource, curated)
 28. │       ├─... %>% distinct()
 29. │       └─OmnipathR:::total_one_resource(resource)
 30. │         └─OmnipathR::import_post_translational_interactions(resources = resource)
 31. │           └─OmnipathR::post_translational(...)
 32. │             ├─rlang::exec(omnipath_query, !!!args)
 33. │             └─OmnipathR (local) `<fn>`(resources = "HPMR", query_type = "interactions", datasets = `<chr>`)
 34. │               └─environment() %>% as.list %>% c(list(...)) %>% ...
 35. ├─dplyr::distinct(.)
 36. ├─dplyr::select(., source, target)
 37. ├─dplyr::inner_join(., curated, by = c("source", "target"))
 38. ├─OmnipathR:::omnipath_check_param(.)
 39. │ └─OmnipathR::resources(param$query_type)
 40. │   └─OmnipathR:::safe_json(path = resources_url)
 41. │     ├─base::suppressWarnings(readLines(con = path, encoding = encoding))
 42. │     │ └─base::withCallingHandlers(...)
 43. │     └─base::readLines(con = path, encoding = encoding)
 44. │       └─base::file(con, "r")
 45. └─base::.handleSimpleError(...)
 46.   └─purrr (local) h(simpleError(msg, call))
 47.     └─cli::cli_abort(...)
 48.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-14_0008/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-03-14 00:31:32 CET ]