[ Started: 2025-02-18 00:17:45 CET ]
[ OmnipathR v3.15.9 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (0a92537 2025-02-13 19:46:14) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/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 ‘3.15.9’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) 
See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:12] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:18:12] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:18:12] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:18:12] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:18:12] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:18:12] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:18:12] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:18:12] [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]
[2025-02-18 00:18:12] [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
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:12] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
ungroup:
  function(x, ...)
ungroup.tbl_attrs:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:22] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:18:22] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:18:22] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:18:22] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:18:22] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:18:22] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:18:22] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:18:22] [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]
[2025-02-18 00:18:22] [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
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:18:22] [TRACE]   [OmnipathR] Cache locked: FALSE
ambiguity_summarize: no visible binding for global variable ‘data’
download_base : fun: no visible binding for global variable
  ‘resp_status_desc’
download_base : fun: no visible global function definition for
  ‘headers’
download_base : fun: no visible binding for global variable ‘response’
log_welcome: no visible binding for global variable ‘pkgname’
translate_ids : <anonymous>: no visible binding for global variable
  ‘From’
xls_downloader: possible error in download_to_cache(url_key = url_key,
  url_key_param = url_key_param, url_param = url_param, ext = ext,
  http_param = http_param, post = post): unused argument (http_param =
  http_param)
Undefined global functions or variables:
  From data headers pkgname resp_status_desc response
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'ambiguity.Rd'
  ‘from_col’ ‘to_col’

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

> ### Name: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2025-02-18 00:21:05] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2025-02-18 00:21:05] [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>
[2025-02-18 00:21:05] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:21:05] [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`.
[2025-02-18 00:21:05] [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`
[2025-02-18 00:21:05] [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`.
[2025-02-18 00:21:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:06] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-02-18 00:21:06] [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`
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:21:06] [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`
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Downloaded 1015 bytes in 0.043393s from www.ensembl.org (22.8 Kb/s); Redirect: 0s, DNS look up: 0.00108s, Connection: 0.019579s, Pretransfer: 0.019631s, First byte at: 0.04331s
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-02-18 00:21:06] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:06] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:06] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <html>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <head>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <style>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] html,
[2025-02-18 00:21:06] [WARN]    [OmnipathR] body {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] padding: 0;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] margin: 0;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] height: 100%;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] body {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] display: grid;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] font-size: 90%;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] h1 {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] h2 {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] h3 {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] header {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] grid-row: header;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] padding: 5px;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] height: 60px;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] background-color: #333366;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] header img {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] width: 185px;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] height: 45px
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] main {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] grid-row: main;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] padding: 20px;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] .mirrors {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] margin-top: 20px;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] padding: 10px;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] footer {
[2025-02-18 00:21:06] [WARN]    [OmnipathR] grid-row: footer;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] padding: 0 20px;
[2025-02-18 00:21:06] [WARN]    [OmnipathR] }
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </style>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </head>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <body>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <header>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </header>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <main>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <p>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-02-18 00:21:06] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-02-18 00:21:06] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </p>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <div class="mirrors">
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <ul>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </ul>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-02-18 00:21:06] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-02-18 00:21:06] [WARN]    [OmnipathR] data centre.
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </div>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </main>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <footer>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] <p>&copy; 2024 EMBL-EBI</p>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </footer>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </body>
[2025-02-18 00:21:06] [WARN]    [OmnipathR] </html>
[2025-02-18 00:21:06] [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 ''
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:27] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:21:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:21:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:21:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:21:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:21:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:21:27] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:21:27] [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]
[2025-02-18 00:21:27] [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
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Contains 14 files.
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:27] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Downloaded 31 Kb in 0.495504s from www.ensembl.org (62.6 Kb/s); Redirect: 0s, DNS look up: 0.001374s, Connection: 0.020183s, Pretransfer: 0.09872s, First byte at: 0.471833s
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:21:28] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.116913s from omabrowser.org (924.1 Kb/s); Redirect: 0s, DNS look up: 0.000852s, Connection: 0.010412s, Pretransfer: 0.048919s, First byte at: 0.061953s
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:21:29] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:29] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:29] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Downloaded 2.2 Mb in 0.447416s from omnipathdb.org (4.8 Mb/s); Redirect: 0s, DNS look up: 0.000987s, Connection: 0.018139s, Pretransfer: 0.05091s, First byte at: 0.085364s
[2025-02-18 00:21:29] [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`
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:29] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-02-18 00:21:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-02-18 00:21:30] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-02-18 00:21:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:30] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:33] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-02-18 00:21:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-02-18 00:21:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:36] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:37] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:37] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Downloaded 906.3 Kb in 0.24592s from omnipathdb.org (3.6 Mb/s); Redirect: 0s, DNS look up: 0.000963s, Connection: 0.019706s, Pretransfer: 0.053161s, First byte at: 0.091983s
[2025-02-18 00:21:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:37] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-18 00:21:37] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:37] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:38] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:39] [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`
[2025-02-18 00:21:39] [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`
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:39] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:39] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.395952s from omnipathdb.org (5.4 Mb/s); Redirect: 0s, DNS look up: 0.000973s, Connection: 0.023896s, Pretransfer: 0.070816s, First byte at: 0.116562s
[2025-02-18 00:21:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:40] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:21:40] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:40] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:42] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:43] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Downloaded 1.4 Mb in 0.264356s from omnipathdb.org (5.5 Mb/s); Redirect: 0s, DNS look up: 0.001019s, Connection: 0.021781s, Pretransfer: 0.073103s, First byte at: 0.115057s
[2025-02-18 00:21:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:43] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-02-18 00:21:43] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:43] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:43] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:44] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Downloaded 1 Mb in 0.186159s from omnipathdb.org (5.6 Mb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.018806s, Pretransfer: 0.052911s, First byte at: 0.086712s
[2025-02-18 00:21:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:44] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-18 00:21:44] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:44] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:44] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:45] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.097231s from omnipathdb.org (617 bytes/s); Redirect: 0s, DNS look up: 0.001376s, Connection: 0.018608s, Pretransfer: 0.079422s, First byte at: 0.097215s
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:45] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-02-18 00:21:45] [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.
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-18 00:21:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:21:46] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-18 00:21:46] [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`
[2025-02-18 00:21:46] [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`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:46] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Downloaded 22.3 Kb in 0.121702s from omnipathdb.org (182.9 Kb/s); Redirect: 0s, DNS look up: 0.001036s, Connection: 0.023244s, Pretransfer: 0.07443s, First byte at: 0.118627s
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:46] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:46] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Downloaded 36.9 Kb in 0.118302s from omnipathdb.org (311.9 Kb/s); Redirect: 0s, DNS look up: 0.001011s, Connection: 0.022477s, Pretransfer: 0.072212s, First byte at: 0.115158s
[2025-02-18 00:21:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:47] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-18 00:21:47] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:47] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:47] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:21:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:21:49] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-02-18 00:21:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:21:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-02-18 00:21:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:49] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-18 00:21:50] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:21:50] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:51] [TRACE]   [OmnipathR] Downloaded 6.1 Mb in 0.70125s from omnipathdb.org (8.6 Mb/s); Redirect: 0s, DNS look up: 0.000981s, Connection: 0.020753s, Pretransfer: 0.054345s, First byte at: 0.094305s
[2025-02-18 00:21:51] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-02-18 00:21:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:51] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-02-18 00:21:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-02-18 00:21:53] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-02-18 00:21:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:53] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:53] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-02-18 00:21:54] [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.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2025-02-18 00:21:54] [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.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-02-18 00:21:54] [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.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.080285s from omnipathdb.org (108.6 Kb/s); Redirect: 0s, DNS look up: 0.000902s, Connection: 0.016607s, Pretransfer: 0.063085s, First byte at: 0.079859s
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-02-18 00:21:54] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:21:54] [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`.
[2025-02-18 00:21:54] [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`
[2025-02-18 00:21:54] [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`.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-18 00:21:54] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:21:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Downloaded 126.2 Kb in 19.224828s from rest.uniprot.org (6.6 Kb/s); Redirect: 0s, DNS look up: 0.00109s, Connection: 0.019659s, Pretransfer: 0.09044s, First byte at: 0.625887s
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-18 00:22:14] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:14] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-02-18 00:22:14] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-02-18 00:22:14] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- 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 ''
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:22:17] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:22:17] [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]
[2025-02-18 00:22:17] [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
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Contains 14 files.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-02-18 00:22:17] [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.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-02-18 00:22:17] [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.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-02-18 00:22:17] [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.
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 00:22:17] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:22:17] [TRACE]   [OmnipathR] Downloaded 31 Kb in 0.382962s from www.ensembl.org (80.9 Kb/s); Redirect: 0s, DNS look up: 0.001329s, Connection: 0.020459s, Pretransfer: 0.095173s, First byte at: 0.365773s
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:18] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.105605s from omabrowser.org (1023 Kb/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.01063s, Pretransfer: 0.043143s, First byte at: 0.055451s
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 00:22:18] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:22:18] [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`
[2025-02-18 00:22:18] [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`
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:22:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:18] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:18] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.272315s from omnipathdb.org (7.8 Mb/s); Redirect: 0s, DNS look up: 0.000863s, Connection: 0.016608s, Pretransfer: 0.054464s, First byte at: 0.086487s
[2025-02-18 00:22:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:19] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:22:19] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:19] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-18 00:22:21] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-02-18 00:22:21] [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>
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:22:21] [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`.
[2025-02-18 00:22:21] [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`
[2025-02-18 00:22:21] [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`.
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:21] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-02-18 00:22:21] [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`
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:22:21] [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`
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Downloaded 1015 bytes in 0.047909s from www.ensembl.org (20.7 Kb/s); Redirect: 0s, DNS look up: 0.001067s, Connection: 0.019573s, Pretransfer: 0.019622s, First byte at: 0.047849s
[2025-02-18 00:22:21] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-02-18 00:22:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-02-18 00:22:22] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-02-18 00:22:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:22] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-02-18 00:22:22] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <html>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <head>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <style>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] html,
[2025-02-18 00:22:22] [WARN]    [OmnipathR] body {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] padding: 0;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] margin: 0;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] height: 100%;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] body {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] display: grid;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] font-size: 90%;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] h1 {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] h2 {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] h3 {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] header {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] grid-row: header;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] padding: 5px;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] height: 60px;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] background-color: #333366;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] header img {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] width: 185px;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] height: 45px
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] main {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] grid-row: main;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] padding: 20px;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] .mirrors {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] margin-top: 20px;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] padding: 10px;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] footer {
[2025-02-18 00:22:22] [WARN]    [OmnipathR] grid-row: footer;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] padding: 0 20px;
[2025-02-18 00:22:22] [WARN]    [OmnipathR] }
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </style>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </head>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <body>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <header>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </header>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <main>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <p>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-02-18 00:22:22] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-02-18 00:22:22] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </p>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <div class="mirrors">
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <ul>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </ul>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-02-18 00:22:22] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-02-18 00:22:22] [WARN]    [OmnipathR] data centre.
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </div>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </main>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <footer>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] <p>&copy; 2024 EMBL-EBI</p>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </footer>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </body>
[2025-02-18 00:22:22] [WARN]    [OmnipathR] </html>
[2025-02-18 00:22:22] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records

Quitting from lines 176-179 [omnipath] (cosmos.Rmd)
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 ''
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:22:23] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:22:23] [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]
[2025-02-18 00:22:23] [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
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Contains 5 files.
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-02-18 00:22:23] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-02-18 00:22:23] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Downloaded 30.6 Kb in 0.377433s from www.ensembl.org (81 Kb/s); Redirect: 0s, DNS look up: 0.001487s, Connection: 0.020105s, Pretransfer: 0.079585s, First byte at: 0.359957s
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:22:24] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:24] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.110395s from omabrowser.org (978.6 Kb/s); Redirect: 0s, DNS look up: 0.000929s, Connection: 0.010707s, Pretransfer: 0.049445s, First byte at: 0.06177s
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:22:25] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:25] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 00:22:25] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:22:25] [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`.
[2025-02-18 00:22:25] [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`
[2025-02-18 00:22:25] [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`.
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:25] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-18 00:22:25] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:25] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:45] [TRACE]   [OmnipathR] Downloaded 126.2 Kb in 20.547878s from rest.uniprot.org (6.1 Kb/s); Redirect: 0s, DNS look up: 0.000986s, Connection: 0.019672s, Pretransfer: 0.103538s, First byte at: 0.974773s
[2025-02-18 00:22:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-02-18 00:22:45] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-02-18 00:22:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:45] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-02-18 00:22:45] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-02-18 00:22:46] [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 ''
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:58] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:22:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:22:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:22:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:22:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:22:58] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:22:58] [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]
[2025-02-18 00:22:58] [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
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Contains 4 files.
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:58] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:59] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Downloaded 30.8 Kb in 0.372972s from www.ensembl.org (82.7 Kb/s); Redirect: 0s, DNS look up: 0.009104s, Connection: 0.02774s, Pretransfer: 0.086984s, First byte at: 0.356669s
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:22:59] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:22:59] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:22:59] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.105207s from omabrowser.org (1 Mb/s); Redirect: 0s, DNS look up: 0.0011s, Connection: 0.010915s, Pretransfer: 0.042986s, First byte at: 0.05605s
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.351541s from omnipathdb.org (6 Mb/s); Redirect: 0s, DNS look up: 0.000954s, Connection: 0.020583s, Pretransfer: 0.076099s, First byte at: 0.114681s
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:00] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:23:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:23:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:23:01] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-18 00:23:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:01] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-18 00:23:03] [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 ''
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:06] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:23:06] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:23:06] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:23:06] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:23:06] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:23:06] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:23:06] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:23:06] [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]
[2025-02-18 00:23:06] [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
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Contains 4 files.
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:23:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Downloaded 30.9 Kb in 0.394035s from www.ensembl.org (78.3 Kb/s); Redirect: 0s, DNS look up: 0.001345s, Connection: 0.020366s, Pretransfer: 0.098308s, First byte at: 0.377125s
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:23:07] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:23:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.119224s from omabrowser.org (906.2 Kb/s); Redirect: 0s, DNS look up: 0.000945s, Connection: 0.01081s, Pretransfer: 0.054666s, First byte at: 0.068497s
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:23:08] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:08] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 00:23:08] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:23:08] [TRACE]   [OmnipathR] Downloaded 3.5 Mb in 0.46206s from omnipathdb.org (7.5 Mb/s); Redirect: 0s, DNS look up: 0.001138s, Connection: 0.020083s, Pretransfer: 0.055187s, First byte at: 0.094542s
[2025-02-18 00:23:08] [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`
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:09] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-02-18 00:23:09] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:23:09] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-02-18 00:23:09] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-02-18 00:23:17] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:28:45] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] Downloaded 1.9 Mb in 0.287302s from omnipathdb.org (6.5 Mb/s); Redirect: 0s, DNS look up: 0.002067s, Connection: 0.019396s, Pretransfer: 0.066487s, First byte at: 0.101441s
[2025-02-18 00:28:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:46] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-02-18 00:28:46] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:46] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-02-18 00:28:46] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-18 00:28:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-18 00:28:47] [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`
[2025-02-18 00:28:47] [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`
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-18 00:28:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Downloaded 5.1 Kb in 0.071758s from omnipathdb.org (71 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.019685s, Pretransfer: 0.052728s, First byte at: 0.071742s
[2025-02-18 00:28:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:47] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-02-18 00:28:47] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:47] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-02-18 00:28:47] [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 ''
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:50] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:28:50] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:28:50] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:28:50] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:28:50] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:28:50] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:28:50] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:28:50] [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]
[2025-02-18 00:28:50] [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
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Contains 6 files.
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:50] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-02-18 00:28:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 00:28:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:28:51] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:28:51] [TRACE]   [OmnipathR] Downloaded 30.9 Kb in 0.385858s from www.ensembl.org (80.2 Kb/s); Redirect: 0s, DNS look up: 0.009104s, Connection: 0.027329s, Pretransfer: 0.082445s, First byte at: 0.368241s
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.110691s from omabrowser.org (976 Kb/s); Redirect: 0s, DNS look up: 0.000921s, Connection: 0.010717s, Pretransfer: 0.04404s, First byte at: 0.058355s
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 00:28:52] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:52] [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`
[2025-02-18 00:28:52] [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`
[2025-02-18 00:28:52] [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`
[2025-02-18 00:28:52] [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`
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:28:52] [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`
[2025-02-18 00:28:52] [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`
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:28:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] Downloaded 1.6 Mb in 0.254154s from omnipathdb.org (6.2 Mb/s); Redirect: 0s, DNS look up: 0.000866s, Connection: 0.02106s, Pretransfer: 0.054207s, First byte at: 0.094998s
[2025-02-18 00:28:53] [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`
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:53] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-02-18 00:28:53] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:28:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:53] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-02-18 00:28:55] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:28:59] [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`
[2025-02-18 00:28:59] [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`
[2025-02-18 00:28:59] [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`
[2025-02-18 00:28:59] [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`
[2025-02-18 00:28:59] [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`
[2025-02-18 00:28:59] [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`
[2025-02-18 00:28:59] [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`
[2025-02-18 00:28:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:28:59] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] Downloaded 1.2 Mb in 0.398368s from omnipathdb.org (3.1 Mb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.019699s, Pretransfer: 0.064039s, First byte at: 0.101677s
[2025-02-18 00:29:00] [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`
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:00] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-02-18 00:29:00] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:00] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:01] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-02-18 00:29:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-02-18 00:29:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-02-18 00:29:01] [TRACE]   [OmnipathR] Organism(s): 10116
[2025-02-18 00:29:01] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:02] [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`
[2025-02-18 00:29:02] [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`
[2025-02-18 00:29:02] [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`
[2025-02-18 00:29:02] [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`
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:02] [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`
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Downloaded 438.4 Kb in 0.183751s from omnipathdb.org (2.3 Mb/s); Redirect: 0s, DNS look up: 0.000893s, Connection: 0.01959s, Pretransfer: 0.07062s, First byte at: 0.108755s
[2025-02-18 00:29:02] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:02] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-02-18 00:29:02] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:02] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:02] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:02] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:03] [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`
[2025-02-18 00:29:03] [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`
[2025-02-18 00:29:03] [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`
[2025-02-18 00:29:03] [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`
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [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`
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Downloaded 188.5 Kb in 0.151671s from omnipathdb.org (1.2 Mb/s); Redirect: 0s, DNS look up: 0.001037s, Connection: 0.022733s, Pretransfer: 0.056247s, First byte at: 0.100298s
[2025-02-18 00:29:03] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:03] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-02-18 00:29:03] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:03] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:03] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [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`
[2025-02-18 00:29:03] [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`
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:03] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.267905s from omnipathdb.org (7.9 Mb/s); Redirect: 0s, DNS look up: 0.00084s, Connection: 0.017747s, Pretransfer: 0.050668s, First byte at: 0.084941s
[2025-02-18 00:29:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:04] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:29:04] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:04] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:06] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Downloaded 264.9 Kb in 0.181079s from omnipathdb.org (1.4 Mb/s); Redirect: 0s, DNS look up: 0.00829s, Connection: 0.028826s, Pretransfer: 0.07568s, First byte at: 0.11692s
[2025-02-18 00:29:08] [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`
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:08] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-02-18 00:29:08] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:08] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:08] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:09] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Downloaded 25.1 Kb in 0.108768s from omnipathdb.org (230.4 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.019643s, Pretransfer: 0.068246s, First byte at: 0.106176s
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:09] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-18 00:29:09] [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`
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:09] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Downloaded 2.2 Kb in 0.085045s from omnipathdb.org (25.4 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.018451s, Pretransfer: 0.067673s, First byte at: 0.085029s
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:09] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:09] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Downloaded 906.3 Kb in 0.22213s from omnipathdb.org (4 Mb/s); Redirect: 0s, DNS look up: 0.000926s, Connection: 0.021392s, Pretransfer: 0.065521s, First byte at: 0.106237s
[2025-02-18 00:29:10] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:10] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-02-18 00:29:10] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:10] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:12] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-02-18 00:29:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:14] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:15] [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`
[2025-02-18 00:29:15] [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`
[2025-02-18 00:29:15] [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`
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:15] [TRACE]   [OmnipathR] Downloaded 446.1 Kb in 0.20114s from omnipathdb.org (2.2 Mb/s); Redirect: 0s, DNS look up: 0.000841s, Connection: 0.020751s, Pretransfer: 0.078142s, First byte at: 0.118518s
[2025-02-18 00:29:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:16] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-02-18 00:29:16] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:16] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:16] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:16] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Downloaded 270.4 Kb in 0.156121s from omnipathdb.org (1.7 Mb/s); Redirect: 0s, DNS look up: 0.000936s, Connection: 0.0207s, Pretransfer: 0.053697s, First byte at: 0.093486s
[2025-02-18 00:29:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:17] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-02-18 00:29:17] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:17] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:17] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2025-02-18 00:29:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:18] [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]
[2025-02-18 00:29:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:18] [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`
[2025-02-18 00:29:18] [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`
[2025-02-18 00:29:18] [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`
[2025-02-18 00:29:18] [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`
[2025-02-18 00:29:18] [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`
[2025-02-18 00:29:18] [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`
[2025-02-18 00:29:18] [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`
[2025-02-18 00:29:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:18] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Downloaded 15 Kb in 0.087884s from omnipathdb.org (170.3 Kb/s); Redirect: 0s, DNS look up: 0.000977s, Connection: 0.018467s, Pretransfer: 0.05188s, First byte at: 0.08755s
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:19] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-02-18 00:29:19] [INFO]    [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1]
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:19] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:19] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records.
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Downloaded 5.8 Kb in 0.086846s from omnipathdb.org (66.9 Kb/s); Redirect: 0s, DNS look up: 0.001062s, Connection: 0.019537s, Pretransfer: 0.064212s, First byte at: 0.086828s
[2025-02-18 00:29:19] [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`
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:19] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-02-18 00:29:19] [INFO]    [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1]
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:19] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:19] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:19] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Downloaded 3.8 Kb in 0.071441s from omnipathdb.org (52.8 Kb/s); Redirect: 0s, DNS look up: 0.000814s, Connection: 0.018949s, Pretransfer: 0.052294s, First byte at: 0.07135s
[2025-02-18 00:29:20] [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`
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1]
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:20] [SUCCESS] [OmnipathR] Downloaded 424 annotation records.
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Downloaded 36.9 Kb in 0.088561s from omnipathdb.org (416.6 Kb/s); Redirect: 0s, DNS look up: 0.000944s, Connection: 0.017867s, Pretransfer: 0.051156s, First byte at: 0.085539s
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:20] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:21] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.077666s from omnipathdb.org (112.2 Kb/s); Redirect: 0s, DNS look up: 0.001006s, Connection: 0.022008s, Pretransfer: 0.055743s, First byte at: 0.077501s
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:21] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:22] [TRACE]   [OmnipathR] Downloaded 4.7 Mb in 0.529431s from omnipathdb.org (9 Mb/s); Redirect: 0s, DNS look up: 0.000953s, Connection: 0.016543s, Pretransfer: 0.058413s, First byte at: 0.090011s
[2025-02-18 00:29:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-02-18 00:29:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:22] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-02-18 00:29:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-02-18 00:29:23] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2025-02-18 00:29:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:23] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:23] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2025-02-18 00:29:24] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-02-18 00:29:24] [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.
[2025-02-18 00:29:24] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2025-02-18 00:29:24] [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 ''
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:17:48 UTC; unix
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:29:26] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:29:26] [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]
[2025-02-18 00:29:26] [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
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Contains 20 files.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 00:29:26] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:29:26] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Preparing httr2 request.
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] HTTP 200
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Downloaded 30.9 Kb in 0.375469s from www.ensembl.org (82.2 Kb/s); Redirect: 0s, DNS look up: 0.001258s, Connection: 0.019622s, Pretransfer: 0.077062s, First byte at: 0.357681s
[2025-02-18 00:29:27] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:27] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:29:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:27] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:29:27] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Downloaded 108 Kb in 0.110056s from omabrowser.org (981.7 Kb/s); Redirect: 0s, DNS look up: 0.001236s, Connection: 0.010616s, Pretransfer: 0.048321s, First byte at: 0.060885s
[2025-02-18 00:29:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Downloaded 29.2 Kb in 0.148649s from omnipathdb.org (196.2 Kb/s); Redirect: 0s, DNS look up: 0.027517s, Connection: 0.047433s, Pretransfer: 0.105822s, First byte at: 0.145308s
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:28] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-02-18 00:29:28] [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`.
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Downloaded 157.2 Kb in 0.095103s from static-content.springer.com (1.6 Mb/s); Redirect: 0s, DNS look up: 0.006786s, Connection: 0.013738s, Pretransfer: 0.046586s, First byte at: 0.080236s
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:28] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:28] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:28] [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`
[2025-02-18 00:29:28] [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`
[2025-02-18 00:29:28] [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`
[2025-02-18 00:29:28] [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`
[2025-02-18 00:29:28] [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`
[2025-02-18 00:29:28] [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`
[2025-02-18 00:29:28] [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`
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:29] [TRACE]   [OmnipathR] Downloaded 2.1 Mb in 0.270339s from omnipathdb.org (7.6 Mb/s); Redirect: 0s, DNS look up: 0.001127s, Connection: 0.018065s, Pretransfer: 0.052313s, First byte at: 0.085984s
[2025-02-18 00:29:29] [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`
[2025-02-18 00:29:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:29] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-02-18 00:29:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-02-18 00:29:30] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-02-18 00:29:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:30] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:33] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-18 00:29:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-18 00:29:33] [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`
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-18 00:29:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-18 00:29:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:33] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:34] [TRACE]   [OmnipathR] Downloaded 2.4 Mb in 0.349877s from omnipathdb.org (6.9 Mb/s); Redirect: 0s, DNS look up: 0.000894s, Connection: 0.020081s, Pretransfer: 0.053852s, First byte at: 0.092343s
[2025-02-18 00:29:34] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-02-18 00:29:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:34] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:35] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Downloaded 110.8 Kb in 0.117177s from omnipathdb.org (945.2 Kb/s); Redirect: 0s, DNS look up: 0.00093s, Connection: 0.016572s, Pretransfer: 0.050496s, First byte at: 0.085205s
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:35] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:35] [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`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Downloaded 310.9 Kb in 0.184992s from omnipathdb.org (1.6 Mb/s); Redirect: 0s, DNS look up: 0.000941s, Connection: 0.021899s, Pretransfer: 0.074522s, First byte at: 0.116484s
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:36] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:36] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Downloaded 251.9 Kb in 0.140735s from omnipathdb.org (1.7 Mb/s); Redirect: 0s, DNS look up: 0.000898s, Connection: 0.017614s, Pretransfer: 0.051321s, First byte at: 0.084925s
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:36] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:36] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:37] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:37] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Downloaded 157.9 Kb in 0.143992s from omnipathdb.org (1.1 Mb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.0185s, Pretransfer: 0.067954s, First byte at: 0.103128s
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:37] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:37] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:37] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:37] [TRACE]   [OmnipathR] Downloaded 306.2 Kb in 0.171054s from omnipathdb.org (1.7 Mb/s); Redirect: 0s, DNS look up: 0.001093s, Connection: 0.018158s, Pretransfer: 0.052151s, First byte at: 0.086928s
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:38] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-02-18 00:29:38] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:38] [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`
[2025-02-18 00:29:38] [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`
[2025-02-18 00:29:38] [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`
[2025-02-18 00:29:38] [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`
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-18 00:29:38] [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`
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:38] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Downloaded 1.5 Mb in 0.221714s from omnipathdb.org (6.8 Mb/s); Redirect: 0s, DNS look up: 0.000854s, Connection: 0.019105s, Pretransfer: 0.06919s, First byte at: 0.106227s
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:38] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-02-18 00:29:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-02-18 00:29:39] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-02-18 00:29:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:39] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:40] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.089483s from omnipathdb.org (146.4 Kb/s); Redirect: 0s, DNS look up: 0.000907s, Connection: 0.01885s, Pretransfer: 0.053292s, First byte at: 0.089209s
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:40] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Downloaded 12.1 Kb in 0.081867s from omnipathdb.org (147.7 Kb/s); Redirect: 0s, DNS look up: 0.000914s, Connection: 0.016306s, Pretransfer: 0.050406s, First byte at: 0.081631s
[2025-02-18 00:29:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:41] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-02-18 00:29:41] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:41] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:41] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-02-18 00:29:41] [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.
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:41] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Downloaded 11.7 Kb in 0.094609s from omnipathdb.org (123.8 Kb/s); Redirect: 0s, DNS look up: 0.000986s, Connection: 0.020597s, Pretransfer: 0.05466s, First byte at: 0.094361s
[2025-02-18 00:29:42] [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`
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:42] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-02-18 00:29:42] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:42] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:42] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Downloaded 1 Mb in 0.207347s from omnipathdb.org (5.1 Mb/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.018501s, Pretransfer: 0.052627s, First byte at: 0.087519s
[2025-02-18 00:29:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:43] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-18 00:29:43] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:43] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:43] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 00:29:44] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Downloaded 20.2 Kb in 0.093098s from omnipathdb.org (216.5 Kb/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.019023s, Pretransfer: 0.053321s, First byte at: 0.090401s
[2025-02-18 00:29:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:44] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-02-18 00:29:44] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:29:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:44] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-02-18 00:29:44] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-02-18 00:29:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-02-18 00:29:46] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-02-18 00:29:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-02-18 00:29:46] [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, 4 WARNINGs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-18_0007/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-02-18 00:29:54 CET ]