[ Started: 2025-05-29 02:35:05 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-3.21/2025-05-29_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
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:34] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:35:34] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:35:34] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:35:34] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:35:34] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:35:34] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:35:34] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:35:34] [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]
[2025-05-29 02:35:34] [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(2025-05-29); 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)
[2025-05-29 02:35:34] [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
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:34] [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
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:44] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:35:44] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:35:44] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:35:44] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:35:44] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:35:44] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:35:44] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:35:44] [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]
[2025-05-29 02:35:44] [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(2025-05-29); 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)
[2025-05-29 02:35:44] [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
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:35:44] [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: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2025-05-29 02:38:10] [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="ensembl_peptide_id"/>
    </Dataset>
</Query>
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:38:10] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-29 02:38:10] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-29 02:38:10] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:38:10] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-05-29 02:38:10] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:38:10] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-29 02:38:10] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 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]
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.04113s from www.ensembl.org (24.1 Kb/s); Redirect: 0s, DNS look up: 6e-05s, Connection: 0.018462s, Pretransfer: 0.018578s, First byte at: 0.041002s
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: A8A3:39575D:C18216:C240AC:68344FD7; Server: GitHub.com; X-Cache-Hits: 3; 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: 14d6d24d6d66b6c75bea984fb5dea91e8f02c357; Content-Encoding: gzip; Date: Thu, 29 May 2025 00:38:10 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600038-LCY; Pragma: no-cache; X-Timer: S1748479090.444711,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 74; Content-Length: 1014
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=A8A3:39575D:C18216:C240AC:68344FD7,Server=GitHub.com,X-Cache-Hits=3,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=14d6d24d6d66b6c75bea984fb5dea91e8f02c357,Content-Encoding=gzip,Date=Thu, 29 May 2025 00:38:10 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600038-LCY,Pragma=no-cache,X-Timer=S1748479090.444711,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=74,Content-Length=1014]
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-05-29 02:38:10] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:38:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:38:10] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2025-05-29 02:38:10] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <html>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <head>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <style>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] html,
[2025-05-29 02:38:10] [WARN]    [OmnipathR] body {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] padding: 0;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] margin: 0;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] height: 100%;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] body {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] display: grid;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] font-size: 90%;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] h1 {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] h2 {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] h3 {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] header {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] grid-row: header;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] padding: 5px;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] height: 60px;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] background-color: #333366;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] header img {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] width: 185px;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] height: 45px
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] main {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] grid-row: main;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] padding: 20px;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] .mirrors {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] margin-top: 20px;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] padding: 10px;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] footer {
[2025-05-29 02:38:10] [WARN]    [OmnipathR] grid-row: footer;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] padding: 0 20px;
[2025-05-29 02:38:10] [WARN]    [OmnipathR] }
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </style>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </head>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <body>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <header>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </header>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <main>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <p>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-05-29 02:38:10] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-05-29 02:38:10] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </p>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <div class="mirrors">
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <ul>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </ul>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-05-29 02:38:10] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-05-29 02:38:10] [WARN]    [OmnipathR] data centre.
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </div>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </main>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <footer>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </footer>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </body>
[2025-05-29 02:38:10] [WARN]    [OmnipathR] </html>
[2025-05-29 02:38:10] [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::ensembl_id_mapping_table("ensp")
 2. │ └─... %>% trim_and_distinct
 3. ├─OmnipathR:::trim_and_distinct(.)
 4. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 5. ├─dplyr::distinct(.)
 6. ├─dplyr::mutate(., across(everything(), str_trim))
 7. ├─rlang::set_names(., c("From", "To"))
 8. └─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 ''
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:39:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:39:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:39:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:39:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:39:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:39:17] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:39:17] [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]
[2025-05-29 02:39:17] [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(2025-05-29); 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)
[2025-05-29 02:39:17] [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
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Contains 14 files.
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-29 02:39:17] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:18] [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]
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Downloaded 31.1 Kb in 0.20787s from www.ensembl.org (149.7 Kb/s); Redirect: 0s, DNS look up: 0.001323s, Connection: 0.019689s, Pretransfer: 0.083765s, First byte at: 0.188533s
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 29 May 2025 00:39:18 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31873; 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=Fri, 30 May 2025 00:39:18 GMT; Set-cookie: ENSEMBL_HINX_SESSION=8c0ad8156caa537d0cd677c46886c6b6002e1f54fe17119eff5aa958; 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=Fri, 30 May 2025 00:39:18 GMT; Set-cookie: ENSEMBL_HINX_SESSION=8c0ad8156caa537d0cd677c46886c6b6002e1f54fe17119eff5aa958; 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
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 29 May 2025 00:39:18 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31873,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=Fri, 30 May 2025 00:39:18 GMT,Set-cookie=ENSEMBL_HINX_SESSION=8c0ad8156caa537d0cd677c46886c6b6002e1f54fe17119eff5aa958; 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=Fri, 30 May 2025 00:39:18 GMT,Set-cookie=ENSEMBL_HINX_SESSION=8c0ad8156caa537d0cd677c46886c6b6002e1f54fe17119eff5aa958; 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]
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:18] [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]
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.059629s from omabrowser.org (145.7 Kb/s); Redirect: 0s, DNS look up: 0.00115s, Connection: 0.011735s, Pretransfer: 0.04406s, First byte at: 0.059487s
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 29 May 2025 00:39:18 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
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:18] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:18] [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`
[2025-05-29 02:39:18] [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`
[2025-05-29 02:39:18] [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`
[2025-05-29 02:39:18] [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`
[2025-05-29 02:39:18] [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`
[2025-05-29 02:39:18] [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`
[2025-05-29 02:39:18] [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`
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:18] [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]
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.104931s from omnipathdb.org (149.3 Kb/s); Redirect: 0s, DNS look up: 0.001003s, Connection: 0.021217s, Pretransfer: 0.063946s, First byte at: 0.104527s
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:19 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:19] [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`
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:19] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-05-29 02:39:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-05-29 02:39:20] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-05-29 02:39:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:20] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:23] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:26] [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]
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105239s from omnipathdb.org (148.9 Kb/s); Redirect: 0s, DNS look up: 0.000989s, Connection: 0.024093s, Pretransfer: 0.057603s, First byte at: 0.104783s
[2025-05-29 02:39:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:27] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:27] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-05-29 02:39:27] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:27] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:28] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:29] [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`
[2025-05-29 02:39:29] [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`
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:29] [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]
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.108069s from omnipathdb.org (145 Kb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.02523s, Pretransfer: 0.058408s, First byte at: 0.107236s
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:29 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:29] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:39:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:39:30] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-29 02:39:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:30] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:32] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:32] [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]
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.114149s from omnipathdb.org (137.2 Kb/s); Redirect: 0s, DNS look up: 0.000971s, Connection: 0.02233s, Pretransfer: 0.070707s, First byte at: 0.113901s
[2025-05-29 02:39:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:33] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-05-29 02:39:33] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:33] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:33] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:33] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:33] [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]
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.119228s from omnipathdb.org (131.4 Kb/s); Redirect: 0s, DNS look up: 0.00097s, Connection: 0.023054s, Pretransfer: 0.074457s, First byte at: 0.118875s
[2025-05-29 02:39:33] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:33 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:33 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:34] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:34] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-29 02:39:34] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:34] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:34] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:34] [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]
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.096279s from omnipathdb.org (623 bytes/s); Redirect: 0s, DNS look up: 0.000944s, Connection: 0.023012s, Pretransfer: 0.072823s, First byte at: 0.096261s
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:35 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 60; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:35 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-05-29 02:39:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:35] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-05-29 02:39:35] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:35] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:35] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-05-29 02:39:35] [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.
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-29 02:39:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:39:35] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:39:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-29 02:39:36] [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`
[2025-05-29 02:39:36] [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`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:36] [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]
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.115506s from omnipathdb.org (135.6 Kb/s); Redirect: 0s, DNS look up: 0.000922s, Connection: 0.021851s, Pretransfer: 0.073391s, First byte at: 0.115125s
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:36] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:36] [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]
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105894s from omnipathdb.org (147.9 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.023839s, Pretransfer: 0.058761s, First byte at: 0.105476s
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:37] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-29 02:39:37] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:37] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:37] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:39:37] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:39:39] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:39] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-29 02:39:39] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:39:39] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:40] [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]
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.119568s from omnipathdb.org (131 Kb/s); Redirect: 0s, DNS look up: 0.000861s, Connection: 0.023277s, Pretransfer: 0.074952s, First byte at: 0.119135s
[2025-05-29 02:39:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-05-29 02:39:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:41] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-05-29 02:39:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-05-29 02:39:43] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-05-29 02:39:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:43] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:43] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-05-29 02:39:43] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-05-29 02:39:43] [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.
[2025-05-29 02:39:43] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2025-05-29 02:39:43] [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.
[2025-05-29 02:39:43] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-05-29 02:39:43] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-05-29 02:39:43] [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.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:44] [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]
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.080954s from omnipathdb.org (107.7 Kb/s); Redirect: 0s, DNS look up: 0.000866s, Connection: 0.023003s, Pretransfer: 0.055859s, First byte at: 0.080778s
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:39:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:39:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-05-29 02:39:44] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:39:44] [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`.
[2025-05-29 02:39:44] [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`
[2025-05-29 02:39:44] [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`.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-29 02:39:44] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:39:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:39:44] [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]
[2025-05-29 02:39:45] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:39:45] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.816946s from rest.uniprot.org (52 bytes/s); Redirect: 0s, DNS look up: 0.000867s, Connection: 0.019867s, Pretransfer: 0.081477s, First byte at: 0.816845s
[2025-05-29 02:39:45] [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: Thu, 29 May 2025 00:39:45 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
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-29 02:40:06] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:06] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:06] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-05-29 02:40:06] [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.
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-05-29 02:40:06] [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.
[2025-05-29 02:40:06] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-05-29 02:40:06] [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 ''
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:40:09] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:40:09] [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]
[2025-05-29 02:40:09] [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(2025-05-29); 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)
[2025-05-29 02:40:09] [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
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Contains 14 files.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-05-29 02:40:09] [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.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-05-29 02:40:09] [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.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-05-29 02:40:09] [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.
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-29 02:40:09] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:09] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.197536s from www.ensembl.org (158 Kb/s); Redirect: 0s, DNS look up: 0.001486s, Connection: 0.019504s, Pretransfer: 0.074635s, First byte at: 0.174658s
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 29 May 2025 00:40:09 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31959; 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=Fri, 30 May 2025 00:40:09 GMT; Set-cookie: ENSEMBL_HINX_SESSION=30fbd1bdd34fb6950b94d3e56886c6e9076cbf0af3f42fcc08dd2961; 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=Fri, 30 May 2025 00:40:09 GMT; Set-cookie: ENSEMBL_HINX_SESSION=30fbd1bdd34fb6950b94d3e56886c6e9076cbf0af3f42fcc08dd2961; 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
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 29 May 2025 00:40:09 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31959,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=Fri, 30 May 2025 00:40:09 GMT,Set-cookie=ENSEMBL_HINX_SESSION=30fbd1bdd34fb6950b94d3e56886c6e9076cbf0af3f42fcc08dd2961; 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=Fri, 30 May 2025 00:40:09 GMT,Set-cookie=ENSEMBL_HINX_SESSION=30fbd1bdd34fb6950b94d3e56886c6e9076cbf0af3f42fcc08dd2961; 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]
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:10] [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]
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.059453s from omabrowser.org (146.2 Kb/s); Redirect: 0s, DNS look up: 0.000808s, Connection: 0.011037s, Pretransfer: 0.044509s, First byte at: 0.059308s
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 29 May 2025 00:40:10 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
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-29 02:40:10] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:10] [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`
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:10] [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]
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096503s from omnipathdb.org (162.3 Kb/s); Redirect: 0s, DNS look up: 0.000903s, Connection: 0.021207s, Pretransfer: 0.055365s, First byte at: 0.096241s
[2025-05-29 02:40:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:40:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:40:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:40:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:11] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:40:11] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:11] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:13] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-05-29 02:40:14] [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>
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:40:14] [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`.
[2025-05-29 02:40:14] [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`
[2025-05-29 02:40:14] [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`.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:14] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-05-29 02:40:14] [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`
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:40:14] [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`
[2025-05-29 02:40:14] [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`.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:14] [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]
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.042452s from www.ensembl.org (23.3 Kb/s); Redirect: 0s, DNS look up: 0.001157s, Connection: 0.019733s, Pretransfer: 0.01978s, First byte at: 0.042391s
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: A8A3:39575D:C18216:C240AC:68344FD7; Server: GitHub.com; X-Cache-Hits: 3; 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: 7bc9c5cf5f4a3ef03f054b40920d0a3e365c10e9; Content-Encoding: gzip; Date: Thu, 29 May 2025 00:40:14 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600029-LCY; Pragma: no-cache; X-Timer: S1748479214.168765,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 198; Content-Length: 1014
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=A8A3:39575D:C18216:C240AC:68344FD7,Server=GitHub.com,X-Cache-Hits=3,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=7bc9c5cf5f4a3ef03f054b40920d0a3e365c10e9,Content-Encoding=gzip,Date=Thu, 29 May 2025 00:40:14 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600029-LCY,Pragma=no-cache,X-Timer=S1748479214.168765,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=198,Content-Length=1014]
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-05-29 02:40:14] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:14] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:14] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <html>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <head>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <style>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] html,
[2025-05-29 02:40:14] [WARN]    [OmnipathR] body {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] padding: 0;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] margin: 0;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] height: 100%;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] body {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] display: grid;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] font-size: 90%;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] h1 {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] h2 {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] h3 {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] header {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] grid-row: header;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] padding: 5px;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] height: 60px;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] background-color: #333366;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] header img {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] width: 185px;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] height: 45px
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] main {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] grid-row: main;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] padding: 20px;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] .mirrors {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] margin-top: 20px;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] padding: 10px;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] footer {
[2025-05-29 02:40:14] [WARN]    [OmnipathR] grid-row: footer;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] padding: 0 20px;
[2025-05-29 02:40:14] [WARN]    [OmnipathR] }
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </style>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </head>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <body>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <header>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </header>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <main>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <p>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-05-29 02:40:14] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-05-29 02:40:14] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </p>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <div class="mirrors">
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <ul>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </ul>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-05-29 02:40:14] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-05-29 02:40:14] [WARN]    [OmnipathR] data centre.
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </div>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </main>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <footer>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </footer>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </body>
[2025-05-29 02:40:14] [WARN]    [OmnipathR] </html>
[2025-05-29 02:40:14] [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 ''
[2025-05-29 02:40:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:15] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:15] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:40:15] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:40:15] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:40:15] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:40:15] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:40:16] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:40:16] [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]
[2025-05-29 02:40:16] [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(2025-05-29); 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)
[2025-05-29 02:40:16] [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
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Contains 5 files.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.188718s from www.ensembl.org (165.4 Kb/s); Redirect: 0s, DNS look up: 0.001367s, Connection: 0.019813s, Pretransfer: 0.074706s, First byte at: 0.165047s
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 29 May 2025 00:40:16 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31961; 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=Fri, 30 May 2025 00:40:16 GMT; Set-cookie: ENSEMBL_HINX_SESSION=27085d88e313a9070bb32eb66886c6f0074b434f08b305bd2e0406da; 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=Fri, 30 May 2025 00:40:16 GMT; Set-cookie: ENSEMBL_HINX_SESSION=27085d88e313a9070bb32eb66886c6f0074b434f08b305bd2e0406da; 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
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 29 May 2025 00:40:16 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31961,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=Fri, 30 May 2025 00:40:16 GMT,Set-cookie=ENSEMBL_HINX_SESSION=27085d88e313a9070bb32eb66886c6f0074b434f08b305bd2e0406da; 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=Fri, 30 May 2025 00:40:16 GMT,Set-cookie=ENSEMBL_HINX_SESSION=27085d88e313a9070bb32eb66886c6f0074b434f08b305bd2e0406da; 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]
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:16] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Downloaded 10 Kb in 0.067019s from omabrowser.org (148.5 Kb/s); Redirect: 0s, DNS look up: 0.000936s, Connection: 0.012554s, Pretransfer: 0.051151s, First byte at: 0.066858s
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 29 May 2025 00:40:17 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
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:17] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:17] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:40:17] [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`.
[2025-05-29 02:40:17] [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`
[2025-05-29 02:40:17] [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`.
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:17] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-29 02:40:17] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:17] [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]
[2025-05-29 02:40:17] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:40:18] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.599757s from rest.uniprot.org (71 bytes/s); Redirect: 0s, DNS look up: 0.001062s, Connection: 0.019513s, Pretransfer: 0.092153s, First byte at: 0.599684s
[2025-05-29 02:40:18] [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: Thu, 29 May 2025 00:40:17 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
[2025-05-29 02:40:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-05-29 02:40:37] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-05-29 02:40:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:37] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:37] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2025-05-29 02:40:38] [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 ''
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:50] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:50] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:40:50] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:40:50] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:40:50] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:40:50] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:40:50] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:40:50] [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]
[2025-05-29 02:40:50] [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(2025-05-29); 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)
[2025-05-29 02:40:50] [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
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Contains 4 files.
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:40:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:51] [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]
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Downloaded 31.1 Kb in 0.179928s from www.ensembl.org (173 Kb/s); Redirect: 0s, DNS look up: 0.0013s, Connection: 0.019451s, Pretransfer: 0.071629s, First byte at: 0.16011s
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 29 May 2025 00:40:51 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31872; 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=Fri, 30 May 2025 00:40:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=4d11aaf84f5a3cba0d64c08c6886c713019cb25cc8eed305ed2c7d1e; 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=Fri, 30 May 2025 00:40:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=4d11aaf84f5a3cba0d64c08c6886c713019cb25cc8eed305ed2c7d1e; 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
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 29 May 2025 00:40:51 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31872,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=Fri, 30 May 2025 00:40:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=4d11aaf84f5a3cba0d64c08c6886c713019cb25cc8eed305ed2c7d1e; 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=Fri, 30 May 2025 00:40:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=4d11aaf84f5a3cba0d64c08c6886c713019cb25cc8eed305ed2c7d1e; 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]
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:51] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:51] [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]
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.057282s from omabrowser.org (151.7 Kb/s); Redirect: 0s, DNS look up: 0.000888s, Connection: 0.010735s, Pretransfer: 0.043308s, First byte at: 0.057141s
[2025-05-29 02:40:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 29 May 2025 00:40:51 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
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:52] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:52] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:52] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:52] [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`
[2025-05-29 02:40:52] [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`
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:52] [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]
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.097235s from omnipathdb.org (161.1 Kb/s); Redirect: 0s, DNS look up: 0.000818s, Connection: 0.022105s, Pretransfer: 0.05532s, First byte at: 0.096894s
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:40:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:40:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:40:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:52] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:40:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:40:53] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-29 02:40:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:53] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-29 02:40:55] [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 ''
[2025-05-29 02:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:58] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:40:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:40:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:40:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:40:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:40:58] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:40:58] [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]
[2025-05-29 02:40:59] [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(2025-05-29); 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)
[2025-05-29 02:40:59] [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
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Contains 4 files.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:59] [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]
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Downloaded 31.1 Kb in 0.200195s from www.ensembl.org (155.4 Kb/s); Redirect: 0s, DNS look up: 0.001446s, Connection: 0.019663s, Pretransfer: 0.072897s, First byte at: 0.181713s
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 29 May 2025 00:40:59 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31865; 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=Fri, 30 May 2025 00:40:59 GMT; Set-cookie: ENSEMBL_HINX_SESSION=244cd40a4413d55608648ed16886c71b049cfd2e4af7147044c19f48; 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=Fri, 30 May 2025 00:40:59 GMT; Set-cookie: ENSEMBL_HINX_SESSION=244cd40a4413d55608648ed16886c71b049cfd2e4af7147044c19f48; 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
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 29 May 2025 00:40:59 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31865,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=Fri, 30 May 2025 00:40:59 GMT,Set-cookie=ENSEMBL_HINX_SESSION=244cd40a4413d55608648ed16886c71b049cfd2e4af7147044c19f48; 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=Fri, 30 May 2025 00:40:59 GMT,Set-cookie=ENSEMBL_HINX_SESSION=244cd40a4413d55608648ed16886c71b049cfd2e4af7147044c19f48; 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]
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:40:59] [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]
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.056977s from omabrowser.org (152.5 Kb/s); Redirect: 0s, DNS look up: 0.001065s, Connection: 0.010875s, Pretransfer: 0.043455s, First byte at: 0.056835s
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 29 May 2025 00:40:59 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
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:40:59] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-29 02:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:41:00] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-29 02:41:00] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:41:00] [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]
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096559s from omnipathdb.org (162.3 Kb/s); Redirect: 0s, DNS look up: 0.000906s, Connection: 0.021254s, Pretransfer: 0.054467s, First byte at: 0.09626s
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:41:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:41:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:41:00] [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`
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:41:00] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:41:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-05-29 02:41:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-05-29 02:41:01] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-05-29 02:41:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:41:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:41:01] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-05-29 02:41:01] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-05-29 02:41:09] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-05-29 02:46:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-05-29 02:46:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:46:36] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:37] [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]
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093402s from omnipathdb.org (167.7 Kb/s); Redirect: 0s, DNS look up: 0.001024s, Connection: 0.02064s, Pretransfer: 0.053455s, First byte at: 0.093077s
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:46:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:46:37 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:46:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:37] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-05-29 02:46:38] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:38] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:38] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-29 02:46:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-29 02:46:38] [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`
[2025-05-29 02:46:38] [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`
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-29 02:46:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:38] [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]
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] Downloaded 5.1 Kb in 0.076411s from omnipathdb.org (66.7 Kb/s); Redirect: 0s, DNS look up: 0.00092s, Connection: 0.021576s, Pretransfer: 0.054304s, First byte at: 0.076377s
[2025-05-29 02:46:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:46:38 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5219; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:46:38 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-05-29 02:46:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:39] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-05-29 02:46:39] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:39] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:39] [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 ''
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:42] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:46:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:46:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:46:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:46:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:46:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:46:42] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:46:42] [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]
[2025-05-29 02:46:42] [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(2025-05-29); 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)
[2025-05-29 02:46:42] [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
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Contains 6 files.
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:42] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:43] [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]
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.222483s from www.ensembl.org (140.2 Kb/s); Redirect: 0s, DNS look up: 0.009157s, Connection: 0.028025s, Pretransfer: 0.081865s, First byte at: 0.20334s
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 29 May 2025 00:46:43 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31946; 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=Fri, 30 May 2025 00:46:43 GMT; Set-cookie: ENSEMBL_HINX_SESSION=1587c89d200fa2ce09633eb76886c873059ba0bc054ac6d3d1200ff4; 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=Fri, 30 May 2025 00:46:43 GMT; Set-cookie: ENSEMBL_HINX_SESSION=1587c89d200fa2ce09633eb76886c873059ba0bc054ac6d3d1200ff4; 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
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 29 May 2025 00:46:43 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31946,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=Fri, 30 May 2025 00:46:43 GMT,Set-cookie=ENSEMBL_HINX_SESSION=1587c89d200fa2ce09633eb76886c873059ba0bc054ac6d3d1200ff4; 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=Fri, 30 May 2025 00:46:43 GMT,Set-cookie=ENSEMBL_HINX_SESSION=1587c89d200fa2ce09633eb76886c873059ba0bc054ac6d3d1200ff4; 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]
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:46:43] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:43] [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]
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.063915s from omabrowser.org (135.9 Kb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.010711s, Pretransfer: 0.049988s, First byte at: 0.063741s
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 29 May 2025 00:46:44 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
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:46:44] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:44] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:44] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:44] [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`
[2025-05-29 02:46:44] [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`
[2025-05-29 02:46:44] [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`
[2025-05-29 02:46:44] [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`
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:44] [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`
[2025-05-29 02:46:44] [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`
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:44] [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]
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094479s from omnipathdb.org (165.8 Kb/s); Redirect: 0s, DNS look up: 0.001049s, Connection: 0.020627s, Pretransfer: 0.053842s, First byte at: 0.093778s
[2025-05-29 02:46:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:46:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:46:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:46:45] [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`
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:45] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-05-29 02:46:45] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:45] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:47] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:51] [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`
[2025-05-29 02:46:51] [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`
[2025-05-29 02:46:51] [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`
[2025-05-29 02:46:51] [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`
[2025-05-29 02:46:51] [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`
[2025-05-29 02:46:51] [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`
[2025-05-29 02:46:51] [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`
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:51] [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]
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.111876s from omnipathdb.org (140 Kb/s); Redirect: 0s, DNS look up: 0.000968s, Connection: 0.021372s, Pretransfer: 0.070411s, First byte at: 0.111605s
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:46:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:46:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:46:52] [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`
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:52] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-05-29 02:46:52] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:52] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:53] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Organism(s): 10116
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:53] [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`
[2025-05-29 02:46:53] [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`
[2025-05-29 02:46:53] [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`
[2025-05-29 02:46:53] [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`
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:53] [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`
[2025-05-29 02:46:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:54] [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]
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093747s from omnipathdb.org (167.1 Kb/s); Redirect: 0s, DNS look up: 0.000938s, Connection: 0.020137s, Pretransfer: 0.054914s, First byte at: 0.093443s
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:46:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:46:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:46:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:54] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-05-29 02:46:54] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:54] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:54] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:54] [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`
[2025-05-29 02:46:54] [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`
[2025-05-29 02:46:54] [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`
[2025-05-29 02:46:54] [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`
[2025-05-29 02:46:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:54] [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`
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.107342s from omnipathdb.org (146 Kb/s); Redirect: 0s, DNS look up: 0.00093s, Connection: 0.019491s, Pretransfer: 0.069606s, First byte at: 0.107039s
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:46:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:46:55 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:46:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:55] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-05-29 02:46:55] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:55] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:55] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:55] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:55] [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`
[2025-05-29 02:46:55] [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`
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:55] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.092947s from omnipathdb.org (168.6 Kb/s); Redirect: 0s, DNS look up: 0.000808s, Connection: 0.020049s, Pretransfer: 0.053605s, First byte at: 0.092627s
[2025-05-29 02:46:55] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:46:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:46:55 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:46:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:56] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:46:56] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:46:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:46:56] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-05-29 02:46:58] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-05-29 02:46:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:46:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-05-29 02:46:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:46:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:46:59] [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`
[2025-05-29 02:46:59] [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`
[2025-05-29 02:46:59] [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`
[2025-05-29 02:46:59] [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`
[2025-05-29 02:46:59] [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`
[2025-05-29 02:46:59] [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`
[2025-05-29 02:46:59] [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`
[2025-05-29 02:46:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:46:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:46:59] [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]
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.116389s from omnipathdb.org (134.6 Kb/s); Redirect: 0s, DNS look up: 0.000919s, Connection: 0.022167s, Pretransfer: 0.074038s, First byte at: 0.116144s
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:00] [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`
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:00] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-05-29 02:47:00] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:00] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:00] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:00] [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`
[2025-05-29 02:47:00] [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`
[2025-05-29 02:47:00] [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`
[2025-05-29 02:47:00] [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`
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:00] [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`
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:00] [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]
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.108141s from omnipathdb.org (144.9 Kb/s); Redirect: 0s, DNS look up: 0.000982s, Connection: 0.019772s, Pretransfer: 0.070327s, First byte at: 0.107856s
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:01] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:01] [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`
[2025-05-29 02:47:01] [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`
[2025-05-29 02:47:01] [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`
[2025-05-29 02:47:01] [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`
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-29 02:47:01] [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`
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Downloaded 2.2 Kb in 0.07777s from omnipathdb.org (27.8 Kb/s); Redirect: 0s, DNS look up: 0.000953s, Connection: 0.021077s, Pretransfer: 0.054573s, First byte at: 0.077744s
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:01 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 2210; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:01 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:01] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:01] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095486s from omnipathdb.org (164.1 Kb/s); Redirect: 0s, DNS look up: 0.000994s, Connection: 0.021262s, Pretransfer: 0.054282s, First byte at: 0.095144s
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:02] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:02] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-05-29 02:47:02] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:02] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:03] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-05-29 02:47:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-29 02:47:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-29 02:47:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:03] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:04] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-05-29 02:47:04] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:06] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:07] [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]
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.089237s from omnipathdb.org (175.6 Kb/s); Redirect: 0s, DNS look up: 0.001063s, Connection: 0.019097s, Pretransfer: 0.052622s, First byte at: 0.088938s
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:07] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-05-29 02:47:08] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:08] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:08] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.125586s from omnipathdb.org (124.8 Kb/s); Redirect: 0s, DNS look up: 0.000967s, Connection: 0.025164s, Pretransfer: 0.077173s, First byte at: 0.125268s
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:09 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:09] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-05-29 02:47:09] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:09] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:09] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations]
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:10] [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]
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] Downloaded 15 Kb in 0.097143s from omnipathdb.org (154.1 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.02181s, Pretransfer: 0.05509s, First byte at: 0.096814s
[2025-05-29 02:47:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1]
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:11] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:11] [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]
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Downloaded 5.8 Kb in 0.077955s from omnipathdb.org (74.5 Kb/s); Redirect: 0s, DNS look up: 0.000898s, Connection: 0.021798s, Pretransfer: 0.055095s, First byte at: 0.077933s
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:11 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5949; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:11 GMT; Cache-Control: public; X-Frame-Options: DENY
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1]
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:11] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:11] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:11] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:12] [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]
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Downloaded 3.8 Kb in 0.078203s from omnipathdb.org (48.2 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.021316s, Pretransfer: 0.054402s, First byte at: 0.077953s
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1]
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:12] [SUCCESS] [OmnipathR] Downloaded 424 annotation records.
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:12] [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]
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093987s from omnipathdb.org (166.7 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.02075s, Pretransfer: 0.05391s, First byte at: 0.093643s
[2025-05-29 02:47:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:13] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.084117s from omnipathdb.org (103.6 Kb/s); Redirect: 0s, DNS look up: 0.000946s, Connection: 0.025157s, Pretransfer: 0.058211s, First byte at: 0.083951s
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:13] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.122813s from omnipathdb.org (127.6 Kb/s); Redirect: 0s, DNS look up: 0.001102s, Connection: 0.024589s, Pretransfer: 0.074739s, First byte at: 0.121826s
[2025-05-29 02:47:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:47:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:47:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:47:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-05-29 02:47:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:14] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:47:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-05-29 02:47:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-05-29 02:47:15] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2025-05-29 02:47:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:15] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2025-05-29 02:47:16] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2025-05-29 02:47:16] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-05-29 02:47:16] [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.
[2025-05-29 02:47:16] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2025-05-29 02:47:16] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2025-05-29 02:47:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:18] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:47:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-05-29 00:34:00 UTC; omnipath
[2025-05-29 02:47:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-05-29 02:47:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-29 00:35:08 UTC; unix
[2025-05-29 02:47:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.99
[2025-05-29 02:47:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-05-29 02:47:18] [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=2025-05-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-05-29 02:47:18] [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]
[2025-05-29 02:47:19] [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(2025-05-29); 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)
[2025-05-29 02:47:19] [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
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Contains 20 files.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-05-29 02:47:19] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:19] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:47:19] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-29 02:47:19] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-29 02:47:19] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-29 02:49:30] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 2m 11.705627s from www.ensembl.org (242 bytes/s); Redirect: 0s, DNS look up: 0.001347s, Connection: 0.019718s, Pretransfer: 0.08873s, First byte at: 2m 11.681706s
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 29 May 2025 00:49:30 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31931; 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=Fri, 30 May 2025 00:48:17 GMT; Set-cookie: ENSEMBL_HINX_SESSION=0ade6ee198d47cb1088530ee6886c91a047d918669ea073072b90942; 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=Fri, 30 May 2025 00:48:17 GMT; Set-cookie: ENSEMBL_HINX_SESSION=0ade6ee198d47cb1088530ee6886c91a047d918669ea073072b90942; 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
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 29 May 2025 00:49:30 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31931,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=Fri, 30 May 2025 00:48:17 GMT,Set-cookie=ENSEMBL_HINX_SESSION=0ade6ee198d47cb1088530ee6886c91a047d918669ea073072b90942; 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=Fri, 30 May 2025 00:48:17 GMT,Set-cookie=ENSEMBL_HINX_SESSION=0ade6ee198d47cb1088530ee6886c91a047d918669ea073072b90942; 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]
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:31] [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]
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.059221s from omabrowser.org (146.7 Kb/s); Redirect: 0s, DNS look up: 0.00098s, Connection: 0.0116s, Pretransfer: 0.044416s, First byte at: 0.059078s
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 29 May 2025 00:49:31 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
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:31] [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]
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.117126s from omnipathdb.org (133.8 Kb/s); Redirect: 0s, DNS look up: 0.00094s, Connection: 0.022875s, Pretransfer: 0.072807s, First byte at: 0.11671s
[2025-05-29 02:49:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:31 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:32] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-05-29 02:49:32] [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`.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:32] [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]
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Downloaded 5.4 Kb in 0.051714s from static-content.springer.com (103.9 Kb/s); Redirect: 0s, DNS look up: 0.001342s, Connection: 0.009161s, Pretransfer: 0.041742s, First byte at: 0.051691s
[2025-05-29 02:49:32] [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: 86115; date: Thu, 29 May 2025 00:49:32 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230129-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1748479772.275695,VS0,VE2; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:32] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:32] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:32] [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`
[2025-05-29 02:49:32] [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`
[2025-05-29 02:49:32] [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`
[2025-05-29 02:49:32] [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`
[2025-05-29 02:49:32] [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`
[2025-05-29 02:49:32] [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`
[2025-05-29 02:49:32] [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`
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:32] [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]
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105161s from omnipathdb.org (149 Kb/s); Redirect: 0s, DNS look up: 0.00098s, Connection: 0.024024s, Pretransfer: 0.058608s, First byte at: 0.104821s
[2025-05-29 02:49:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:33] [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`
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:33] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-05-29 02:49:33] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:33] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:36] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-05-29 02:49:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-05-29 02:49:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:36] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-29 02:49:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-29 02:49:37] [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`
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-29 02:49:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:37] [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]
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095535s from omnipathdb.org (164 Kb/s); Redirect: 0s, DNS look up: 0.001012s, Connection: 0.01763s, Pretransfer: 0.061879s, First byte at: 0.0951s
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:37 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:37] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-05-29 02:49:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-05-29 02:49:38] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-05-29 02:49:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:38] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:38] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:39] [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]
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.106295s from omnipathdb.org (147.4 Kb/s); Redirect: 0s, DNS look up: 0.000975s, Connection: 0.024623s, Pretransfer: 0.058016s, First byte at: 0.105889s
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:39] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:39] [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`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:39] [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]
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105637s from omnipathdb.org (148.3 Kb/s); Redirect: 0s, DNS look up: 0.000961s, Connection: 0.024513s, Pretransfer: 0.058062s, First byte at: 0.105234s
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:39] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:40] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:40] [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]
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095382s from omnipathdb.org (164.3 Kb/s); Redirect: 0s, DNS look up: 0.000927s, Connection: 0.021189s, Pretransfer: 0.054474s, First byte at: 0.095005s
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:40] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:40] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:40] [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]
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105036s from omnipathdb.org (149.2 Kb/s); Redirect: 0s, DNS look up: 0.000916s, Connection: 0.024004s, Pretransfer: 0.057387s, First byte at: 0.104663s
[2025-05-29 02:49:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:41] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:41] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.084718s from omnipathdb.org (184.9 Kb/s); Redirect: 0s, DNS look up: 0.000959s, Connection: 0.017429s, Pretransfer: 0.050937s, First byte at: 0.084427s
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:41] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-05-29 02:49:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-05-29 02:49:41] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:42] [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`
[2025-05-29 02:49:42] [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`
[2025-05-29 02:49:42] [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`
[2025-05-29 02:49:42] [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`
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-29 02:49:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-29 02:49:42] [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`
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095597s from omnipathdb.org (163.9 Kb/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.019516s, Pretransfer: 0.057924s, First byte at: 0.095221s
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:42 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:42] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-05-29 02:49:42] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:42] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:43] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:43] [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]
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.113536s from omnipathdb.org (115.4 Kb/s); Redirect: 0s, DNS look up: 0.000868s, Connection: 0.020803s, Pretransfer: 0.073164s, First byte at: 0.113283s
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:44] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:44] [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]
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Downloaded 12.1 Kb in 0.101741s from omnipathdb.org (118.9 Kb/s); Redirect: 0s, DNS look up: 0.000878s, Connection: 0.021454s, Pretransfer: 0.060311s, First byte at: 0.101481s
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:44] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:44] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-05-29 02:49:45] [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.
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:45] [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`
[2025-05-29 02:49:45] [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`
[2025-05-29 02:49:45] [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`
[2025-05-29 02:49:45] [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`
[2025-05-29 02:49:45] [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`
[2025-05-29 02:49:45] [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`
[2025-05-29 02:49:45] [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`
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:45] [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]
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] Downloaded 11.7 Kb in 0.106947s from omnipathdb.org (109.5 Kb/s); Redirect: 0s, DNS look up: 0.001008s, Connection: 0.024948s, Pretransfer: 0.058463s, First byte at: 0.106686s
[2025-05-29 02:49:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:45 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:46] [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`
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:46] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-05-29 02:49:46] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:46] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:46] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:46] [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]
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.113856s from omnipathdb.org (137.6 Kb/s); Redirect: 0s, DNS look up: 0.000999s, Connection: 0.022919s, Pretransfer: 0.069222s, First byte at: 0.113488s
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:47] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-29 02:49:47] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:47] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:47] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-29 02:49:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-05-29 02:49:47] [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]
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.107494s from omnipathdb.org (145.7 Kb/s); Redirect: 0s, DNS look up: 0.000913s, Connection: 0.021486s, Pretransfer: 0.065754s, First byte at: 0.107133s
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 29 May 2025 00:49:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 29 May 2025 01:49:48 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-29 02:49:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:48] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-05-29 02:49:48] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-29 02:49:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:48] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-05-29 02:49:48] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-05-29 02:49:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-05-29 02:49:50] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-05-29 02:49:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-05-29 02:49:50] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’

SUMMARY: processing the following file failed:
  ‘cosmos.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-05-29_0219/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-05-29 02:49:59 CEST ]