[ Started: 2025-07-29 19:08:38 CEST ]
[ OmnipathR v3.17.4 for BioC-3.22 from https://github.com/saezlab/OmnipathR@devel (a7f3b9d 2025-07-16 16:03:35) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.17.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-07-29 17:07:29 UTC; omnipath
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-29 17:08:40 UTC; unix
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-07-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-07-29 19:09:08] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-07-29 19:09:08] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-07-29); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-29 19:09:08] [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
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:08] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-07-29 17:07:29 UTC; omnipath
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-29 17:08:40 UTC; unix
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-07-29; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-07-29 19:09:19] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-07-29 19:09:19] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-07-29); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-29 19:09:19] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:09:19] [TRACE]   [OmnipathR] Cache locked: FALSE
taxon_names_table: no visible binding for global variable
  ‘latin_name_uniprot’
taxon_names_table: no visible binding for global variable
  ‘latin_name_ensembl’
taxon_names_table: no visible binding for global variable
  ‘latin_name_oma’
taxon_names_table: no visible binding for global variable
  ‘common_name_ensembl’
taxon_names_table: no visible binding for global variable
  ‘common_name_uniprot’
Undefined global functions or variables:
  common_name_ensembl common_name_uniprot latin_name_ensembl
  latin_name_oma latin_name_uniprot
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: curated_ligrec_stats
> ### Title: Statistics about literature curated ligand-receptor interactions
> ### Aliases: curated_ligrec_stats
> 
> ### ** Examples
> 
> clr <- curated_ligrec_stats()
Warning in import_post_translational_interactions(resources = ., ...) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions]
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2025-07-29 19:11:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:32] [SUCCESS] [OmnipathR] Loaded 4568 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions]
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2025-07-29 19:11:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-07-29 19:11:32] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions]
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2025-07-29 19:11:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:32] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-07-29 19:11:33] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions]
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2025-07-29 19:11:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:33] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-07-29 19:11:33] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions]
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2025-07-29 19:11:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-07-29 19:11:34] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2025-07-29 19:11:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:34] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations]
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:34] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2025-07-29 19:11:35] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.112636s from omnipathdb.org (139.1 Kb/s); Redirect: 0s, DNS look up: 0.000939s, Connection: 0.021271s, Pretransfer: 0.07168s, First byte at: 0.112348s
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 29 Jul 2025 17:11:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 29 Jul 2025 18:11:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `unknown` to `started`.
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Download ready [key=afe18d85fba82fa7d5f390113de328e13aa85e89, version=1]
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:35] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `started` to `ready`.
[2025-07-29 19:11:35] [SUCCESS] [OmnipathR] Downloaded 2879 interactions.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:35] [TRACE]   [OmnipathR] Orthology targets: 
Warning in readLines(con = path, encoding = encoding) :
  incomplete final line found on 'https://omnipathdb.org/resources'
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2025-07-29 19:11:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-07-29 19:11:36] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
Warning in import_post_translational_interactions(resources = resource) :
  'import_post_translational_interactions' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions]
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-07-29 19:11:36] [TRACE]   [OmnipathR] Orthology targets: 
Warning in file(con, "r") :
  URL 'https://omnipathdb.org/resources': Timeout of 60 seconds was reached
Error in `map()`:
ℹ In index: 1.
Caused by error in `map()`:
ℹ In index: 3.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `file()`:
! cannot open the connection to 'https://omnipathdb.org/resources'
Backtrace:
     ▆
  1. ├─OmnipathR::curated_ligrec_stats()
  2. │ └─... %>% unnest_wider(col = data)
  3. ├─OmnipathR:::unnest_wider(., col = data)
  4. │ └─base::eval(call[[tbl_name]], parent.frame())
  5. │   └─base::eval(call[[tbl_name]], parent.frame())
  6. ├─tibble::tibble(resource = names(.), data = .)
  7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
  8. │   └─rlang::eval_tidy(xs[[j]], mask)
  9. ├─rlang::set_names(map(., stats_one_resource, curated), .)
 10. ├─purrr::map(., stats_one_resource, curated)
 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 12. │   ├─purrr:::with_indexed_errors(...)
 13. │   │ └─base::withCallingHandlers(...)
 14. │   ├─purrr:::call_with_cleanup(...)
 15. │   └─OmnipathR (local) .f(.x[[i]], ...)
 16. │     └─... %>% ...
 17. ├─purrr::map(., nrow)
 18. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 19. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
 20. ├─rlang::set_names(...)
 21. ├─purrr::map(...)
 22. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 23. │   ├─purrr:::with_indexed_errors(...)
 24. │   │ └─base::withCallingHandlers(...)
 25. │   ├─purrr:::call_with_cleanup(...)
 26. │   └─OmnipathR (local) .f(.x[[i]], ...)
 27. │     └─get(sprintf("%s_one_resource", field))(resource, curated)
 28. │       ├─... %>% with_references(resources = resource)
 29. │       └─OmnipathR::import_post_translational_interactions(resources = resource)
 30. │         └─OmnipathR::post_translational(...)
 31. │           ├─rlang::exec(omnipath_query, !!!args)
 32. │           └─OmnipathR (local) `<fn>`(...)
 33. │             └─environment() %>% as.list %>% c(list(...)) %>% ...
 34. ├─OmnipathR::with_references(., resources = resource)
 35. │ └─... %>% distinct(across(everything()))
 36. ├─dplyr::distinct(., across(everything()))
 37. ├─dplyr::bind_rows(.)
 38. │ └─rlang::list2(...)
 39. ├─purrr::map(., .with_references, data = data)
 40. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 41. │   ├─purrr:::with_indexed_errors(...)
 42. │   │ └─base::withCallingHandlers(...)
 43. │   ├─purrr:::call_with_cleanup(...)
 44. │   └─OmnipathR (local) .f(.x[[i]], ...)
 45. │     └─data %>% filter(predicate(references))
 46. ├─dplyr::filter(., predicate(references))
 47. ├─OmnipathR:::omnipath_check_param(.)
 48. │ └─OmnipathR::resources(param$query_type)
 49. │   └─OmnipathR:::safe_json(path = resources_url)
 50. │     └─base::readLines(con = path, encoding = encoding)
 51. │       └─base::file(con, "r")
 52. └─base::.handleSimpleError(...)
 53.   └─purrr (local) h(simpleError(msg, call))
 54.     └─cli::cli_abort(...)
 55.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-07-29_1858/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-07-29 19:24:56 CEST ]