[ Started: 2025-05-27 02:30:14 CEST ]
[ OmnipathR v3.15.99 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (02b2582 2025-05-22 13:00:44) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/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 ‘3.15.99’
* 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 ... OK
* 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
[2025-05-27 02:30:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:30:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:42] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:30:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:30:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:30:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:30:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:30:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:30:43] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:30:43] [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]
[2025-05-27 02:30:43] [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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:30:43] [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
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:30:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:43] [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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:53] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:30:53] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:30:53] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:30:53] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:30:53] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:30:53] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:30:53] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:30:53] [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]
[2025-05-27 02:30:53] [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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:30:53] [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
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:30:53] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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: omnipath_for_cosmos
> ### Title: OmniPath PPI for the COSMOS PKN
> ### Aliases: omnipath_for_cosmos
> 
> ### ** Examples
> 
> op_cosmos <- omnipath_for_cosmos()
[2025-05-27 02:37:26] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:37:26] [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]
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.11071s from omnipathdb.org (141.5 Kb/s); Redirect: 0s, DNS look up: 0.000888s, Connection: 0.022122s, Pretransfer: 0.068802s, First byte at: 0.110459s
[2025-05-27 02:37:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:37:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:37:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:37:27] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:27] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:37:27] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:27] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-27 02:37:29] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 02:37:29] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:29] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-05-27 02:37:29] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:37:29] [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]
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:37:29] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.053522s from www.ensembl.org (18.5 Kb/s); Redirect: 0s, DNS look up: 0.008257s, Connection: 0.026411s, Pretransfer: 0.026495s, First byte at: 0.053379s
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: A8A3:39575D:C18216:C240AC:68344FD7; Server: GitHub.com; X-Cache-Hits: 1; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: 08019e62ce9b963733439f15bea02e1c67547b3b; Content-Encoding: gzip; Date: Tue, 27 May 2025 00:37:30 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600041-LCY; Pragma: no-cache; X-Timer: S1748306250.026295,VS0,VE1; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 169; Content-Length: 1014
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=A8A3:39575D:C18216:C240AC:68344FD7,Server=GitHub.com,X-Cache-Hits=1,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=08019e62ce9b963733439f15bea02e1c67547b3b,Content-Encoding=gzip,Date=Tue, 27 May 2025 00:37:30 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600041-LCY,Pragma=no-cache,X-Timer=S1748306250.026295,VS0,VE1,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=169,Content-Length=1014]
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-05-27 02:37:30] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:30] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-05-27 02:37:30] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <html>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <head>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <style>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] html,
[2025-05-27 02:37:30] [WARN]    [OmnipathR] body {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] padding: 0;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] margin: 0;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] height: 100%;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] body {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] display: grid;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] font-size: 90%;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] h1 {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] h2 {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] h3 {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] header {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] grid-row: header;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] padding: 5px;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] height: 60px;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] background-color: #333366;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] header img {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] width: 185px;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] height: 45px
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] main {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] grid-row: main;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] padding: 20px;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] .mirrors {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] margin-top: 20px;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] padding: 10px;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] footer {
[2025-05-27 02:37:30] [WARN]    [OmnipathR] grid-row: footer;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] padding: 0 20px;
[2025-05-27 02:37:30] [WARN]    [OmnipathR] }
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </style>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </head>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <body>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <header>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </header>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <main>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <p>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-05-27 02:37:30] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-05-27 02:37:30] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </p>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <div class="mirrors">
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <ul>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </ul>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-05-27 02:37:30] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-05-27 02:37:30] [WARN]    [OmnipathR] data centre.
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </div>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </main>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <footer>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </footer>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </body>
[2025-05-27 02:37:30] [WARN]    [OmnipathR] </html>
[2025-05-27 02:37:30] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
     ▆
  1. ├─OmnipathR::omnipath_for_cosmos()
  2. │ └─... %T>% ...
  3. ├─dplyr::bind_rows(...)
  4. │ └─rlang::list2(...)
  5. ├─OmnipathR::translate_ids_multi(...)
  6. │ └─source_cols %>% seq_along %>% ...
  7. ├─purrr::reduce(...)
  8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
  9. │   └─OmnipathR (local) fn(out, elt, ...)
 10. │     └─OmnipathR::translate_ids(...)
 11. │       └─... %>% ...
 12. ├─purrr::reduce2(...)
 13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
 14. │   └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
 15. │     ├─... %>% ...
 16. │     └─OmnipathR:::id_translation_table(...)
 17. │       └─OmnipathR::ensembl_id_mapping_table(...)
 18. │         └─... %>% trim_and_distinct
 19. ├─OmnipathR:::ensure_character(., From, To)
 20. │ └─d %>% mutate(across(c(!!!cols), as.character))
 21. ├─dplyr::mutate(., across(c(!!!cols), as.character))
 22. ├─OmnipathR:::trim_and_distinct(.)
 23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 24. ├─dplyr::distinct(.)
 25. ├─dplyr::mutate(., across(everything(), str_trim))
 26. ├─rlang::set_names(., c("From", "To"))
 27. └─rlang::abort(message = message)
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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:48] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:37:48] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:37:48] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:37:48] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:37:48] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:37:48] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:37:48] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:37:48] [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]
[2025-05-27 02:37:48] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:37:48] [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
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Contains 14 files.
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:48] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.206243s from www.ensembl.org (151.1 Kb/s); Redirect: 0s, DNS look up: 0.001387s, Connection: 0.01985s, Pretransfer: 0.088243s, First byte at: 0.181781s
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 27 May 2025 00:37:49 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31913; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:37:49 GMT; Set-cookie: ENSEMBL_HINX_SESSION=526361531f2719c50e994fd96884235d02ffdac31f747e9a3402a2b4; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:37:49 GMT; Set-cookie: ENSEMBL_HINX_SESSION=526361531f2719c50e994fd96884235d02ffdac31f747e9a3402a2b4; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 27 May 2025 00:37:49 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31913,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:37:49 GMT,Set-cookie=ENSEMBL_HINX_SESSION=526361531f2719c50e994fd96884235d02ffdac31f747e9a3402a2b4; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:37:49 GMT,Set-cookie=ENSEMBL_HINX_SESSION=526361531f2719c50e994fd96884235d02ffdac31f747e9a3402a2b4; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-35.ebi.ac.uk]
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.06525s from omabrowser.org (133.2 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.012684s, Pretransfer: 0.049998s, First byte at: 0.064885s
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 27 May 2025 00:37:49 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:37:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.1021s from omnipathdb.org (153.4 Kb/s); Redirect: 0s, DNS look up: 0.000981s, Connection: 0.023094s, Pretransfer: 0.056983s, First byte at: 0.101711s
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:37:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:37:50 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:37:50] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:50] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:37:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-05-27 02:37:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-05-27 02:37:51] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-05-27 02:37:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:51] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-05-27 02:37:54] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:37:57] [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]
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.102391s from omnipathdb.org (153 Kb/s); Redirect: 0s, DNS look up: 0.001133s, Connection: 0.023544s, Pretransfer: 0.056919s, First byte at: 0.102045s
[2025-05-27 02:37:57] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:37:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:37:57 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:37:58] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:58] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-05-27 02:37:58] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:37:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:37:58] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-05-27 02:37:59] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-05-27 02:37:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:37:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-05-27 02:37:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:37:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:37:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:00] [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]
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10169s from omnipathdb.org (154.1 Kb/s); Redirect: 0s, DNS look up: 0.000767s, Connection: 0.022428s, Pretransfer: 0.056271s, First byte at: 0.10079s
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:00] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:00] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:38:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:38:01] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-27 02:38:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:01] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:03] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:03] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:03] [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]
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.113654s from omnipathdb.org (137.8 Kb/s); Redirect: 0s, DNS look up: 0.000995s, Connection: 0.021484s, Pretransfer: 0.071285s, First byte at: 0.112954s
[2025-05-27 02:38:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:03 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:04] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-05-27 02:38:04] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:04] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:04] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:04] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:04] [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]
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100899s from omnipathdb.org (155.3 Kb/s); Redirect: 0s, DNS look up: 0.000943s, Connection: 0.022806s, Pretransfer: 0.056577s, First byte at: 0.100518s
[2025-05-27 02:38:04] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:05] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-27 02:38:05] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:05] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:05] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.080969s from omnipathdb.org (741 bytes/s); Redirect: 0s, DNS look up: 0.001038s, Connection: 0.02339s, Pretransfer: 0.056985s, First byte at: 0.080951s
[2025-05-27 02:38:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:05 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 60; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:05 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:06] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-05-27 02:38:06] [FATAL]   [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:38:06] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:06] [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]
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.103746s from omnipathdb.org (151 Kb/s); Redirect: 0s, DNS look up: 0.000963s, Connection: 0.023458s, Pretransfer: 0.057194s, First byte at: 0.103327s
[2025-05-27 02:38:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:07] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105338s from omnipathdb.org (148.7 Kb/s); Redirect: 0s, DNS look up: 0.000881s, Connection: 0.023726s, Pretransfer: 0.058447s, First byte at: 0.10453s
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:07] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:07] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:08] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:38:08] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:10] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-27 02:38:10] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-27 02:38:10] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.103969s from omnipathdb.org (150.7 Kb/s); Redirect: 0s, DNS look up: 0.000848s, Connection: 0.023713s, Pretransfer: 0.057409s, First byte at: 0.103492s
[2025-05-27 02:38:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-05-27 02:38:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:12] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-05-27 02:38:14] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:14] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:14] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:38:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:15] [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]
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.099s from omnipathdb.org (88 Kb/s); Redirect: 0s, DNS look up: 0.000884s, Connection: 0.02353s, Pretransfer: 0.075086s, First byte at: 0.09883s
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:15] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-27 02:38:15] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:15] [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]
[2025-05-27 02:38:16] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:38:16] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.64961s from rest.uniprot.org (66 bytes/s); Redirect: 0s, DNS look up: 0.00105s, Connection: 0.019672s, Pretransfer: 0.073675s, First byte at: 0.64954s
[2025-05-27 02:38:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Tue, 27 May 2025 00:38:16 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-27 02:38:36] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:36] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:36] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-05-27 02:38:36] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:37] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-05-27 02:38:37] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:38:39] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:38:39] [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]
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:38:39] [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
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Contains 14 files.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-27 02:38:39] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:39] [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]
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:38:39] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Downloaded 31.1 Kb in 0.215274s from www.ensembl.org (144.6 Kb/s); Redirect: 0s, DNS look up: 0.001269s, Connection: 0.01971s, Pretransfer: 0.093717s, First byte at: 0.190337s
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 27 May 2025 00:38:39 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31875; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:38:39 GMT; Set-cookie: ENSEMBL_HINX_SESSION=0df07dd4316958ed0a8baaf76884238f06ed0a808a0cb22bfc5de771; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:38:39 GMT; Set-cookie: ENSEMBL_HINX_SESSION=0df07dd4316958ed0a8baaf76884238f06ed0a808a0cb22bfc5de771; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 27 May 2025 00:38:39 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31875,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:38:39 GMT,Set-cookie=ENSEMBL_HINX_SESSION=0df07dd4316958ed0a8baaf76884238f06ed0a808a0cb22bfc5de771; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:38:39 GMT,Set-cookie=ENSEMBL_HINX_SESSION=0df07dd4316958ed0a8baaf76884238f06ed0a808a0cb22bfc5de771; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-35.ebi.ac.uk]
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.06708s from omabrowser.org (129.5 Kb/s); Redirect: 0s, DNS look up: 0.000958s, Connection: 0.012577s, Pretransfer: 0.051886s, First byte at: 0.066937s
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 27 May 2025 00:38:40 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-27 02:38:40] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.09919s from omnipathdb.org (157.9 Kb/s); Redirect: 0s, DNS look up: 0.001065s, Connection: 0.021276s, Pretransfer: 0.058742s, First byte at: 0.098877s
[2025-05-27 02:38:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:38:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:38:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:38:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:41] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:38:41] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:41] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-27 02:38:43] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 02:38:44] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:38:44] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-05-27 02:38:44] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:38:44] [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]
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:38:44] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:43:44] [WARN]    [OmnipathR] Failed to download `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` (attempt 1/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]: Operation timed out after 300002 milliseconds with 0 bytes received
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Attempt 2/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.052675s from www.ensembl.org (18.8 Kb/s); Redirect: 0s, DNS look up: 0.010156s, Connection: 0.029353s, Pretransfer: 0.029573s, First byte at: 0.052538s
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: A8A3:39575D:C18216:C240AC:68344FD7; Server: GitHub.com; X-Cache-Hits: 1; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: 59ad7737de23279f63562bb6e3f80af136f63fac; Content-Encoding: gzip; Date: Tue, 27 May 2025 00:43:49 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600027-LCY; Pragma: no-cache; X-Timer: S1748306629.309064,VS0,VE1; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 549; Content-Length: 1014
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=A8A3:39575D:C18216:C240AC:68344FD7,Server=GitHub.com,X-Cache-Hits=1,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=59ad7737de23279f63562bb6e3f80af136f63fac,Content-Encoding=gzip,Date=Tue, 27 May 2025 00:43:49 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600027-LCY,Pragma=no-cache,X-Timer=S1748306629.309064,VS0,VE1,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=549,Content-Length=1014]
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-05-27 02:43:49] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:49] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-05-27 02:43:49] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <html>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <head>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <style>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] html,
[2025-05-27 02:43:49] [WARN]    [OmnipathR] body {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] padding: 0;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] margin: 0;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] height: 100%;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] body {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] display: grid;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] font-size: 90%;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] h1 {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] h2 {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] h3 {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] header {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] grid-row: header;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] padding: 5px;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] height: 60px;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] background-color: #333366;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] header img {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] width: 185px;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] height: 45px
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] main {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] grid-row: main;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] padding: 20px;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] .mirrors {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] margin-top: 20px;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] padding: 10px;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] footer {
[2025-05-27 02:43:49] [WARN]    [OmnipathR] grid-row: footer;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] padding: 0 20px;
[2025-05-27 02:43:49] [WARN]    [OmnipathR] }
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </style>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </head>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <body>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <header>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </header>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <main>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <p>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-05-27 02:43:49] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-05-27 02:43:49] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </p>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <div class="mirrors">
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <ul>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </ul>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-05-27 02:43:49] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-05-27 02:43:49] [WARN]    [OmnipathR] data centre.
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </div>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </main>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <footer>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </footer>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </body>
[2025-05-27 02:43:49] [WARN]    [OmnipathR] </html>
[2025-05-27 02:43:49] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records

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

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

--- re-building ‘db_manager.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:43:51] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:43:51] [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]
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:43:51] [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
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Contains 5 files.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-27 02:43:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:43:51] [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]
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:43:51] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Downloaded 31.3 Kb in 0.232396s from www.ensembl.org (134.5 Kb/s); Redirect: 0s, DNS look up: 0.00135s, Connection: 0.019957s, Pretransfer: 0.073944s, First byte at: 0.21326s
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 27 May 2025 00:43:51 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32001; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:43:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=665775f2169a3834086aba04688424c7040c5390c9a14791fbe3dfe3; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:43:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=665775f2169a3834086aba04688424c7040c5390c9a14791fbe3dfe3; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-31.ebi.ac.uk
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 27 May 2025 00:43:51 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32001,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:43:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=665775f2169a3834086aba04688424c7040c5390c9a14791fbe3dfe3; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:43:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=665775f2169a3834086aba04688424c7040c5390c9a14791fbe3dfe3; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-31.ebi.ac.uk]
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.058714s from omabrowser.org (148 Kb/s); Redirect: 0s, DNS look up: 0.00109s, Connection: 0.011726s, Pretransfer: 0.044823s, First byte at: 0.05857s
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 27 May 2025 00:43:52 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-27 02:43:52] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:43:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:43:53] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:43:53] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.596932s from rest.uniprot.org (72 bytes/s); Redirect: 0s, DNS look up: 0.008158s, Connection: 0.027078s, Pretransfer: 0.08175s, First byte at: 0.596873s
[2025-05-27 02:43:53] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Tue, 27 May 2025 00:43:53 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025
[2025-05-27 02:44:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-27 02:44:15] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-05-27 02:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:15] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-05-27 02:44:15] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2025-05-27 02:44:15] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:44:28] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:44:28] [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]
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:44:28] [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
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Contains 4 files.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-27 02:44:28] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:44:28] [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]
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:44:28] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.220681s from www.ensembl.org (141.4 Kb/s); Redirect: 0s, DNS look up: 0.001319s, Connection: 0.019939s, Pretransfer: 0.090612s, First byte at: 0.201959s
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 27 May 2025 00:44:29 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31945; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:28 GMT; Set-cookie: ENSEMBL_HINX_SESSION=b80fc09fae693b39089d165d688424ec04fbe4326938a20c9e0c7576; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:28 GMT; Set-cookie: ENSEMBL_HINX_SESSION=b80fc09fae693b39089d165d688424ec04fbe4326938a20c9e0c7576; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-34.ebi.ac.uk
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 27 May 2025 00:44:29 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31945,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:28 GMT,Set-cookie=ENSEMBL_HINX_SESSION=b80fc09fae693b39089d165d688424ec04fbe4326938a20c9e0c7576; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:28 GMT,Set-cookie=ENSEMBL_HINX_SESSION=b80fc09fae693b39089d165d688424ec04fbe4326938a20c9e0c7576; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-34.ebi.ac.uk]
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:44:29] [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]
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.063833s from omabrowser.org (136.1 Kb/s); Redirect: 0s, DNS look up: 0.00097s, Connection: 0.011674s, Pretransfer: 0.049862s, First byte at: 0.063688s
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 27 May 2025 00:44:29 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:44:29] [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]
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.118125s from omnipathdb.org (132.6 Kb/s); Redirect: 0s, DNS look up: 0.010092s, Connection: 0.031282s, Pretransfer: 0.074958s, First byte at: 0.117814s
[2025-05-27 02:44:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:44:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:44:29 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:44:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:30] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:44:30] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:30] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-27 02:44:33] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:44:36] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:44:36] [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]
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:44:36] [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
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Contains 4 files.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-27 02:44:36] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:44:36] [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]
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:44:36] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.199028s from www.ensembl.org (156.8 Kb/s); Redirect: 0s, DNS look up: 0.00136s, Connection: 0.019595s, Pretransfer: 0.076334s, First byte at: 0.175302s
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 27 May 2025 00:44:36 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31957; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:36 GMT; Set-cookie: ENSEMBL_HINX_SESSION=79c0ff01da3662cf0ae02f2b688424f40686db45218b60d1fe1ad06a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:36 GMT; Set-cookie: ENSEMBL_HINX_SESSION=79c0ff01da3662cf0ae02f2b688424f40686db45218b60d1fe1ad06a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-31.ebi.ac.uk
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 27 May 2025 00:44:36 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31957,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:36 GMT,Set-cookie=ENSEMBL_HINX_SESSION=79c0ff01da3662cf0ae02f2b688424f40686db45218b60d1fe1ad06a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:44:36 GMT,Set-cookie=ENSEMBL_HINX_SESSION=79c0ff01da3662cf0ae02f2b688424f40686db45218b60d1fe1ad06a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-31.ebi.ac.uk]
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:44:37] [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]
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.061293s from omabrowser.org (141.8 Kb/s); Redirect: 0s, DNS look up: 0.001095s, Connection: 0.012682s, Pretransfer: 0.046562s, First byte at: 0.061149s
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 27 May 2025 00:44:37 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:44:37] [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]
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101663s from omnipathdb.org (154.1 Kb/s); Redirect: 0s, DNS look up: 0.000922s, Connection: 0.023173s, Pretransfer: 0.056902s, First byte at: 0.101328s
[2025-05-27 02:44:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:44:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:44:37 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:44:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-05-27 02:44:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:38] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:44:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-05-27 02:44:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-05-27 02:44:39] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-05-27 02:44:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:44:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:44:39] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-05-27 02:44:39] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-05-27 02:44:47] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-05-27 02:50:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-05-27 02:50:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100937s from omnipathdb.org (155.2 Kb/s); Redirect: 0s, DNS look up: 0.001019s, Connection: 0.023129s, Pretransfer: 0.057451s, First byte at: 0.100636s
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:11 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:11] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:12] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:12] [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]
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Downloaded 5.1 Kb in 0.086337s from omnipathdb.org (59 Kb/s); Redirect: 0s, DNS look up: 0.000916s, Connection: 0.019128s, Pretransfer: 0.067966s, First byte at: 0.086319s
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:12 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5219; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:12 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:12] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:12] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:16] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:50:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:50:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:50:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:50:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:50:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:50:16] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:50:16] [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]
[2025-05-27 02:50:16] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:50:16] [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
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Contains 6 files.
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:16] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.188098s from www.ensembl.org (165.7 Kb/s); Redirect: 0s, DNS look up: 0.006201s, Connection: 0.024815s, Pretransfer: 0.076015s, First byte at: 0.164259s
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 27 May 2025 00:50:17 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31925; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:50:17 GMT; Set-cookie: ENSEMBL_HINX_SESSION=b4b61532d1b2df930c9aae6a6884264900fdebcbabc2af7940796453; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:50:17 GMT; Set-cookie: ENSEMBL_HINX_SESSION=b4b61532d1b2df930c9aae6a6884264900fdebcbabc2af7940796453; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-33.ebi.ac.uk
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 27 May 2025 00:50:17 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31925,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:50:17 GMT,Set-cookie=ENSEMBL_HINX_SESSION=b4b61532d1b2df930c9aae6a6884264900fdebcbabc2af7940796453; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:50:17 GMT,Set-cookie=ENSEMBL_HINX_SESSION=b4b61532d1b2df930c9aae6a6884264900fdebcbabc2af7940796453; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-33.ebi.ac.uk]
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:50:17] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.063995s from omabrowser.org (135.8 Kb/s); Redirect: 0s, DNS look up: 0.00087s, Connection: 0.011565s, Pretransfer: 0.050037s, First byte at: 0.063552s
[2025-05-27 02:50:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 27 May 2025 00:50:17 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:18] [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]
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.11923s from omnipathdb.org (131.4 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.023294s, Pretransfer: 0.074124s, First byte at: 0.118895s
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:18 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:18] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-05-27 02:50:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-05-27 02:50:19] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-05-27 02:50:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:19] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:20] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:25] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:25] [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]
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094725s from omnipathdb.org (165.4 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.021057s, Pretransfer: 0.054109s, First byte at: 0.094453s
[2025-05-27 02:50:25] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:25 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:26] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-05-27 02:50:26] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:26] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:27] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Organism(s): 10116
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:27] [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]
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10623s from omnipathdb.org (147.5 Kb/s); Redirect: 0s, DNS look up: 0.000919s, Connection: 0.020868s, Pretransfer: 0.06568s, First byte at: 0.105925s
[2025-05-27 02:50:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:27 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:28] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-05-27 02:50:28] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:28] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:28] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:28] [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]
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.102933s from omnipathdb.org (152.2 Kb/s); Redirect: 0s, DNS look up: 0.001022s, Connection: 0.023708s, Pretransfer: 0.056865s, First byte at: 0.102564s
[2025-05-27 02:50:28] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:28 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:29] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:29] [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]
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.120133s from omnipathdb.org (130.4 Kb/s); Redirect: 0s, DNS look up: 0.030216s, Connection: 0.048404s, Pretransfer: 0.083312s, First byte at: 0.119882s
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:29 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:29] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:50:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-27 02:50:30] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-27 02:50:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:30] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:32] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:33] [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]
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.106391s from omnipathdb.org (297.6 Kb/s); Redirect: 0s, DNS look up: 0.000996s, Connection: 0.022646s, Pretransfer: 0.056302s, First byte at: 0.105626s
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:33 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:33 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:33] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:34] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:34] [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]
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093832s from omnipathdb.org (167 Kb/s); Redirect: 0s, DNS look up: 0.001093s, Connection: 0.019828s, Pretransfer: 0.055747s, First byte at: 0.093517s
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:34 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:34] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:34] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:50:34] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Downloaded 2.2 Kb in 0.076402s from omnipathdb.org (28.2 Kb/s); Redirect: 0s, DNS look up: 0.001055s, Connection: 0.021627s, Pretransfer: 0.0552s, First byte at: 0.076386s
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:50:35 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 2210; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:50:35 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-05-27 02:50:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:35] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-05-27 02:50:35] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:50:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:50:35] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-05-27 02:50:35] [SUCCESS] [OmnipathR] Downloaded 32 interactions.

Quitting from omnipath_intro.Rmd:496-536 [PTMs]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://omnipathdb.org/resources'
---
Backtrace:
    ▆
 1. └─OmnipathR::enzsub_resources()
 2.   └─OmnipathR::resources(query_type = "enzsub", datasets = dataset)
 3.     └─OmnipathR:::safe_json(path = resources_url)
 4.       └─base::readLines(con = path, encoding = encoding)
 5.         └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
cannot open the connection to 'https://omnipathdb.org/resources'
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-27 00:29:08 UTC; omnipath
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-27 00:30:17 UTC; unix
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-27 02:51:37] [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=2025-05-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-27 02:51:37] [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]
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.15.99(2025-05-27); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 02:51:37] [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
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Contains 11 files.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:37] [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]
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.187884s from www.ensembl.org (166 Kb/s); Redirect: 0s, DNS look up: 0.001234s, Connection: 0.019868s, Pretransfer: 0.073242s, First byte at: 0.163949s
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 27 May 2025 00:51:37 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31934; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:51:37 GMT; Set-cookie: ENSEMBL_HINX_SESSION=c3e96e39894d25420b3b615968842699075c38817b65ab28a28f993f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:51:37 GMT; Set-cookie: ENSEMBL_HINX_SESSION=c3e96e39894d25420b3b615968842699075c38817b65ab28a28f993f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-33.ebi.ac.uk
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 27 May 2025 00:51:37 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31934,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:51:37 GMT,Set-cookie=ENSEMBL_HINX_SESSION=c3e96e39894d25420b3b615968842699075c38817b65ab28a28f993f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 28 May 2025 00:51:37 GMT,Set-cookie=ENSEMBL_HINX_SESSION=c3e96e39894d25420b3b615968842699075c38817b65ab28a28f993f; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-33.ebi.ac.uk]
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:37] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-27 02:51:37] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:38] [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]
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.057746s from omabrowser.org (150.5 Kb/s); Redirect: 0s, DNS look up: 0.000886s, Connection: 0.011614s, Pretransfer: 0.044034s, First byte at: 0.057597s
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 27 May 2025 00:51:38 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:38] [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]
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101671s from omnipathdb.org (154.1 Kb/s); Redirect: 0s, DNS look up: 0.000963s, Connection: 0.019696s, Pretransfer: 0.063545s, First byte at: 0.101295s
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:38 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:38] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-05-27 02:51:38] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-05-27 02:51:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:39] [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]
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Downloaded 10.8 Kb in 0.079653s from static-content.springer.com (135 Kb/s); Redirect: 0s, DNS look up: 0.001795s, Connection: 0.008794s, Pretransfer: 0.040717s, First byte at: 0.079624s
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; cache-control: private, max-age=86400; last-modified: Thu, 16 Nov 2023 16:51:13 GMT; etag: "daa03c1eafd00cad9456b660ca85b849"; x-goog-generation: 1700153472991609; x-goog-metageneration: 1; x-goog-stored-content-encoding: identity; x-goog-stored-content-length: 160972; content-type: application/octet-stream; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; x-guploader-uploadid: AFiumC7ZpYKgxNZtW8bqZY8u8z2x9V62Ud4hs7Wz5zewS1xt8QPnURGT01ram66yNo-OgPW_uOsydnKUF6Xmdbs; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 0; date: Tue, 27 May 2025 00:51:39 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230101-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1748307099.052506,VS0,VE31; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-05-27 02:51:39] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:39] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:39] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:39] [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]
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.124016s from omnipathdb.org (126.3 Kb/s); Redirect: 0s, DNS look up: 0.001035s, Connection: 0.024594s, Pretransfer: 0.075898s, First byte at: 0.123251s
[2025-05-27 02:51:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:40] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-05-27 02:51:40] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:40] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:43] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-05-27 02:51:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-05-27 02:51:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:44] [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]
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.107154s from omnipathdb.org (146.2 Kb/s); Redirect: 0s, DNS look up: 0.001068s, Connection: 0.024984s, Pretransfer: 0.057723s, First byte at: 0.106613s
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:44] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-05-27 02:51:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-05-27 02:51:45] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-05-27 02:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:45] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:45] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:46] [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]
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096695s from omnipathdb.org (162 Kb/s); Redirect: 0s, DNS look up: 0.000998s, Connection: 0.021802s, Pretransfer: 0.054737s, First byte at: 0.096297s
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:46] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:46] [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]
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.09594s from omnipathdb.org (163.3 Kb/s); Redirect: 0s, DNS look up: 0.000844s, Connection: 0.021408s, Pretransfer: 0.054005s, First byte at: 0.095477s
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:46] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:46] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.114805s from omnipathdb.org (136.5 Kb/s); Redirect: 0s, DNS look up: 0.000996s, Connection: 0.021892s, Pretransfer: 0.072406s, First byte at: 0.114446s
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:47 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:47] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:47] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.115751s from omnipathdb.org (135.4 Kb/s); Redirect: 0s, DNS look up: 0.001024s, Connection: 0.022606s, Pretransfer: 0.072064s, First byte at: 0.115377s
[2025-05-27 02:51:47] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:47 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:48] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:48] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:48] [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]
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094219s from omnipathdb.org (166.3 Kb/s); Redirect: 0s, DNS look up: 0.00112s, Connection: 0.021053s, Pretransfer: 0.053833s, First byte at: 0.093858s
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:48 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:48] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:48] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-27 02:51:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-27 02:51:48] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096732s from omnipathdb.org (162 Kb/s); Redirect: 0s, DNS look up: 0.001005s, Connection: 0.021494s, Pretransfer: 0.054635s, First byte at: 0.096368s
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:49 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:49] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:49] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-05-27 02:51:49] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:49] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:50] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-05-27 02:51:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-05-27 02:51:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:51] [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]
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.106294s from omnipathdb.org (123.3 Kb/s); Redirect: 0s, DNS look up: 0.000941s, Connection: 0.024616s, Pretransfer: 0.057895s, First byte at: 0.10597s
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:51] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:51] [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]
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Downloaded 12.1 Kb in 0.090117s from omnipathdb.org (134.2 Kb/s); Redirect: 0s, DNS look up: 0.000974s, Connection: 0.019391s, Pretransfer: 0.052567s, First byte at: 0.089837s
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:51] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:51] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] Downloaded 11.7 Kb in 0.105829s from omnipathdb.org (110.6 Kb/s); Redirect: 0s, DNS look up: 0.000921s, Connection: 0.01976s, Pretransfer: 0.068344s, First byte at: 0.105605s
[2025-05-27 02:51:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:53] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:53] [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]
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.114024s from omnipathdb.org (137.4 Kb/s); Redirect: 0s, DNS look up: 0.000986s, Connection: 0.021819s, Pretransfer: 0.072389s, First byte at: 0.113656s
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:53 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:53] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-27 02:51:54] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:54] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:54] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-27 02:51:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.119696s from omnipathdb.org (130.9 Kb/s); Redirect: 0s, DNS look up: 0.001005s, Connection: 0.023882s, Pretransfer: 0.073446s, First byte at: 0.11929s
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 27 May 2025 00:51:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 27 May 2025 01:51:55 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-27 02:51:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:55] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-05-27 02:51:55] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 02:51:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:55] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-05-27 02:51:55] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-27 02:51:57] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-27 02:51:57] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:57] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-05-27 02:51:57] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-27 02:51:57] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘cosmos.Rmd’ ‘omnipath_intro.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-27_0219/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-05-27 02:52:06 CEST ]