[ Started: 2025-05-08 23:02:55 CEST ]
[ OmnipathR v3.14.0 for BioC-3.20 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_20 (3c7d7f1 2024-10-29 10:41:00) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* 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 ‘3.14.0’
* 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 ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:20] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:29] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:03:29] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
> 
> ### ** Examples
> 
> organism_for(10116, 'chalmers-gem')
Error in organism_for(10116, "chalmers-gem") : 
  Organism `10116` (common_name: `Norway rat - BN/NHsdMcwi`; common_name: `Norway rat - BN/NHsdMcwi`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758), Caenorhabditis elegans (Nematode, N2).
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
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Contains 14 files.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-05-08 23:09:27] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:09:27] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-08 23:09:27] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:09:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:27] [WARN]    [OmnipathR] HTTP 504
[2025-05-08 23:10:27] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504
[2025-05-08 23:10:32] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:32] [TRACE]   [OmnipathR] HTTP 200
[2025-05-08 23:10:32] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-08 23:10:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:32] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from bioc_workshop.Rmd:215-218 [network]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Contains 2 files.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-05-08 23:10:34] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-08 23:10:34] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] HTTP 200
[2025-05-08 23:10:34] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:34] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

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

Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Contains 2 files.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] HTTP 200
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:36] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from db_manager.Rmd:66-69 [get]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'db_manager.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Contains 2 files.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-05-08 23:10:38] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-08 23:10:38] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] HTTP 200
[2025-05-08 23:10:38] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:38] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from drug_targets.Rmd:45-51 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'drug_targets.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Contains 2 files.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-05-08 23:10:40] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-08 23:10:40] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] HTTP 200
[2025-05-08 23:10:40] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:40] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from extra_attrs.Rmd:55-58 [load-interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:43] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Contains 2 files.
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:43] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-05-08 23:10:44] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:44] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:44] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-08 23:10:44] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] HTTP 200
[2025-05-08 23:10:44] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:44] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from omnipath_intro.Rmd:166-175 [interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Contains 2 files.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-05-08 23:10:45] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:45] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-08 23:10:45] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-08 23:10:45] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-08 23:10:46] [TRACE]   [OmnipathR] HTTP 200
[2025-05-08 23:10:46] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-08 23:10:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-08 23:10:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-08 23:10:46] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from paths.Rmd:55-67 [tfcensus-op]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'paths.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- failed re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘db_manager.Rmd’ ‘drug_targets.Rmd’
  ‘extra_attrs.Rmd’ ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-05-08_2254/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-05-08 23:10:53 CEST ]