[ Started: 2026-02-11 03:39:01 CET ]
[ OmnipathR v3.19.6 for BioC-3.22 from https://github.com/saezlab/OmnipathR@devel (4c56371 2026-01-29 16:23:53) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/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 ‘3.19.6’
* 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
[2026-02-11 03:39:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:39:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:32] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-11 03:39:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-11 02:36:12 UTC; omnipath
[2026-02-11 03:39:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-11 03:39:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-11 02:39:04 UTC; unix
[2026-02-11 03:39:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-11 03:39:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-11 03:39:32] [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=2026-02-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-11 03:39:32] [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]
[2026-02-11 03:39:33] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-11); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-11 03:39:33] [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
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-11 03:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:33] [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 ... WARNING
'::' or ':::' import not declared from: ‘SBMLR’
'loadNamespace' or 'requireNamespace' call not declared from: ‘SBMLR’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-02-11 03:39:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:39:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:43] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-11 03:39:43] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-11 02:36:12 UTC; omnipath
[2026-02-11 03:39:43] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-11 03:39:43] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-11 02:39:04 UTC; unix
[2026-02-11 03:39:43] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-11 03:39:43] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-11 03:39:43] [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=2026-02-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-11 03:39:43] [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]
[2026-02-11 03:39:44] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-11); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-11 03:39:44] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:39:44] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘git_repo’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘git_host’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘gem_info’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘latest_version’
metabolic_atlas_model: no visible binding for global variable ‘path’
metabolic_atlas_model : silent_sbml: no visible binding for global
  variable ‘result’
metabolic_atlas_models: no visible binding for global variable ‘id’
patch_httr2_keep_handle: no visible binding for global variable
  ‘handle’
patch_httr2_keep_handle: no visible global function definition for
  ‘ORIGINAL’
Undefined global functions or variables:
  ORIGINAL enzyme_genesymbol gem_info git_host git_repo handle id
  latest_version path result
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'load_db.Rd':
load_db
  Code: function(key, param = list(), reload = FALSE)
  Docs: function(key, param = list())
  Argument names in code not in docs:
    reload

* 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: metabolic_atlas_list_models
> ### Title: List of original GEMs in Metabolic Atlas
> ### Aliases: metabolic_atlas_list_models
> 
> ### ** Examples
> 
> metabolic_atlas_models()
[2026-02-11 03:48:00] [WARN]    [OmnipathR] SBMLR package not available, install with: BiocManager::install('SBMLR')
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:00] [INFO]    [OmnipathR] Looking up in cache `https://metabolicatlas.org/api/v2/repository/models/`: key=035dd3150b56361f57dd12fb4ecb7f1416d31ddf, no version available.
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:00] [INFO]    [OmnipathR] Created new version for cache record 035dd3150b56361f57dd12fb4ecb7f1416d31ddf: version 1.
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/035dd3150b56361f57dd12fb4ecb7f1416d31ddf-1
[2026-02-11 03:48:00] [INFO]    [OmnipathR] Retrieving URL: `https://metabolicatlas.org/api/v2/repository/models/`
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://metabolicatlas.org/api/v2/repository/models/`
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://metabolicatlas.org/api/v2/repository/models/`.
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] HTTP headers: <NULL>
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] HTTP headers: []
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Downloaded 32.8 Kb in 0.210185s from metabolicatlas.org (155.9 Kb/s); Redirect: 0s, DNS look up: 0.038296s, Connection: 0.042488s, Pretransfer: 0.097424s, First byte at: 0.203776s
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 11 Feb 2026 02:48:00 GMT; content-type: application/json; charset=utf-8; server: cloudflare; x-powered-by: Express; etag: W/"7b9e6-L2oww6jQElU58qCfhBAtYNT1rHA"; strict-transport-security: max-age=63072000; includeSubdomains;; x-frame-options: DENY; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=H2%2BWgp703HjKYxRCK3b45d3U6G2LaBdFKZe0wZS5xol%2BKYd1kWBF4NkHPQp9W1UMAk68gDngSVvAe2oUnQSLfo5PSLcO9ctA08R9QP1BOWQCvQ%3D%3D"}]}; cf-ray: 9cc0865cc8a76e96-STR; alt-svc: h3=":443"; ma=86400
[2026-02-11 03:48:00] [TRACE]   [OmnipathR] Response headers: [date=Wed, 11 Feb 2026 02:48:00 GMT,content-type=application/json; charset=utf-8,server=cloudflare,x-powered-by=Express,etag=W/"7b9e6-L2oww6jQElU58qCfhBAtYNT1rHA",strict-transport-security=max-age=63072000; includeSubdomains;,x-frame-options=DENY,content-encoding=gzip,cf-cache-status=DYNAMIC,vary=accept-encoding,nel={"report_to":"cf-nel","success_fraction":0.0,"max_age":604800},report-to={"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=H2%2BWgp703HjKYxRCK3b45d3U6G2LaBdFKZe0wZS5xol%2BKYd1kWBF4NkHPQp9W1UMAk68gDngSVvAe2oUnQSLfo5PSLcO9ctA08R9QP1BOWQCvQ%3D%3D"}]},cf-ray=9cc0865cc8a76e96-STR,alt-svc=h3=":443"; ma=86400]
[2026-02-11 03:48:01] [INFO]    [OmnipathR] Download ready [key=035dd3150b56361f57dd12fb4ecb7f1416d31ddf, version=1]
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:01] [INFO]    [OmnipathR] Cache item `035dd3150b56361f57dd12fb4ecb7f1416d31ddf` version 1: status changed from `unknown` to `ready`.
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/035dd3150b56361f57dd12fb4ecb7f1416d31ddf-1` (encoding: UTF-8).
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:01] [INFO]    [OmnipathR] Downloading model: INIT normal models [id=1,organism=Homo sapiens,tissue=Breast,cell_type=Myoepithelial cells,condition=Healthy,reaction_count=4772,metabolite_count=4046,gene_count=1776,year=2014]
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:01] [INFO]    [OmnipathR] Looking up in cache `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`: key=7852b38b808236483c3516bf8c7cc803b60135ff, no version available.
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:01] [INFO]    [OmnipathR] Created new version for cache record 7852b38b808236483c3516bf8c7cc803b60135ff: version 1.
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7852b38b808236483c3516bf8c7cc803b60135ff-1
[2026-02-11 03:48:01] [INFO]    [OmnipathR] Downloading `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-11 03:48:01] [INFO]    [OmnipathR] Retrieving URL: `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`.
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] HTTP headers: <NULL>
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] HTTP headers: []
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] Downloaded 351.5 Kb in 0.093809s from metabolicatlas.org (3.7 Mb/s); Redirect: 0s, DNS look up: 3.3e-05s, Connection: 0s, Pretransfer: 0.000101s, First byte at: 0.0818s
[2026-02-11 03:48:01] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 11 Feb 2026 02:48:01 GMT; content-type: application/zip; server: cloudflare; x-powered-by: Express; cache-control: public, max-age=1382400; last-modified: Sat, 06 Sep 2025 22:47:44 GMT; etag: W/"5a69b-1992136d0d2"; strict-transport-security: max-age=63072000; includeSubdomains;; x-frame-options: DENY; content-encoding: gzip; cf-cache-status: REVALIDATED; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=vTNYoS9pgLa3DQ%2BHDh8ugYO1uGNd7aD0zoZDCRYUsPdBCdLT3aVASRx4sEtQJW6PMCO15nh7XltRdD4O8tMPX4oFjvE0jiLIClnlbYIAxE203A%3D%3D"}]}; cf-ray: 9cc086637a066e96-STR; alt-svc: h3=":443"; ma=86400
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] Response headers: [date=Wed, 11 Feb 2026 02:48:01 GMT,content-type=application/zip,server=cloudflare,x-powered-by=Express,cache-control=public, max-age=1382400,last-modified=Sat, 06 Sep 2025 22:47:44 GMT,etag=W/"5a69b-1992136d0d2",strict-transport-security=max-age=63072000; includeSubdomains;,x-frame-options=DENY,content-encoding=gzip,cf-cache-status=REVALIDATED,vary=accept-encoding,nel={"report_to":"cf-nel","success_fraction":0.0,"max_age":604800},report-to={"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=vTNYoS9pgLa3DQ%2BHDh8ugYO1uGNd7aD0zoZDCRYUsPdBCdLT3aVASRx4sEtQJW6PMCO15nh7XltRdD4O8tMPX4oFjvE0jiLIClnlbYIAxE203A%3D%3D"}]},cf-ray=9cc086637a066e96-STR,alt-svc=h3=":443"; ma=86400]
[2026-02-11 03:48:02] [INFO]    [OmnipathR] Download ready [key=7852b38b808236483c3516bf8c7cc803b60135ff, version=1]
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:02] [INFO]    [OmnipathR] Cache item `7852b38b808236483c3516bf8c7cc803b60135ff` version 1: status changed from `unknown` to `ready`.
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] Archive type `zip`: `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-11 03:48:02] [INFO]    [OmnipathR] Looking up in cache `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`: key=7852b38b808236483c3516bf8c7cc803b60135ff, latest version=1.
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7852b38b808236483c3516bf8c7cc803b60135ff-1.zip
[2026-02-11 03:48:02] [TRACE]   [OmnipathR] Path in archive: `breast_-_myoepithelial_cells_2.xml`
[2026-02-11 03:48:02] [INFO]    [OmnipathR] Downloading model: Bacteria models [id=2,organism=Streptomyces coelicolor,tissue=NA,cell_type=NA,condition=Evaluating metabolic capabilities,reaction_count=971,metabolite_count=500,gene_count=711,year=2005]
Error in `map()`:
ℹ In index: 2.
Caused by error in `pmap()`:
! Can't recycle `.l[[1]]` (size 0) to match `.l[[2]]` (size 2).
Backtrace:
     ▆
  1. ├─OmnipathR::metabolic_atlas_models()
  2. │ └─... %>% ...
  3. ├─purrr::map(...)
  4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │   ├─purrr:::with_indexed_errors(...)
  6. │   │ └─base::withCallingHandlers(...)
  7. │   ├─purrr:::call_with_cleanup(...)
  8. │   └─OmnipathR (local) .f(.x[[i]], ...)
  9. │     └─OmnipathR:::metabolic_atlas_model(slice(models, .x), return_xml = return_xml)
 10. │       ├─rlang::exec(method, !!!dl_args)
 11. │       └─OmnipathR (local) `<fn>`(...)
 12. │         └─OmnipathR:::archive_downloader(...)
 13. │           └─OmnipathR::omnipath_cache_latest_or_new(url = cache_url, post = cache_post)
 14. │             └─OmnipathR::omnipath_cache_get(...)
 15. │               └─OmnipathR:::omnipath_cache_ensure_key(...)
 16. │                 └─OmnipathR::omnipath_cache_key(url = url, post = post, payload = payload)
 17. │                   └─... %>% map_chr(digest::sha1_digest)
 18. ├─purrr::map_chr(., digest::sha1_digest)
 19. │ └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
 20. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
 21. ├─purrr::pmap(., list)
 22. │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
 23. │   └─vctrs::vec_size_common(!!!.l, .arg = ".l", .call = .purrr_error_call)
 24. └─vctrs::stop_incompatible_size(...)
 25.   └─vctrs:::stop_incompatible(...)
 26.     └─vctrs:::stop_vctrs(...)
 27.       └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
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 WARNINGs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-11_0326/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2026-02-11 04:01:16 CET ]