[ Started: 2024-01-11 12:07:20 CET ]
[ decoupleR v2.6.0 for BioC-3.17 from https://github.com/saezlab/decoupleR@RELEASE_3_17 ]

* using log directory ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.6.0’
* 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 ‘decoupleR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc       5.9Mb
    extdata   1.5Mb
* checking package directory ... OK
* checking ‘build’ 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 R 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 dependencies in R code ... NOTE
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:07:44] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Contains 5 files.
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:07:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-01-11 12:07:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:07:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-01-11 12:07:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:07:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-01-11 12:07:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:07:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-01-11 12:07:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:07:45] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘decoupleR.Rmd’ using ‘UTF-8’... OK
  ‘pw_bk.Rmd’ using ‘UTF-8’... OK
  ‘pw_sc.Rmd’ using ‘UTF-8’... OK
  ‘tf_bk.Rmd’ using ‘UTF-8’... OK
  ‘tf_sc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘decoupleR.Rmd’ using rmarkdown
The magick package is required to crop "/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck/vign_test/decoupleR/vignettes/decoupleR_files/figure-html/show_matrix-1.png" but not available.
The magick package is required to crop "/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck/vign_test/decoupleR/vignettes/decoupleR_files/figure-html/res_gsea-1.png" but not available.
The magick package is required to crop "/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck/vign_test/decoupleR/vignettes/decoupleR_files/figure-html/res_ulm-1.png" but not available.
The magick package is required to crop "/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck/vign_test/decoupleR/vignettes/decoupleR_files/figure-html/res_decouple-1.png" but not available.
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Contains 8 files.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:22] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-01-11 12:25:22] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:23] [TRACE]   [OmnipathR] HTTP 200
[2024-01-11 12:25:23] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-01-11 12:25:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:23] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from lines 101-103 [progeny] (pw_bk.Rmd)
Error: processing vignette 'pw_bk.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 ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
The magick package is required to crop "/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck/vign_test/decoupleR/vignettes/pw_sc_files/figure-html/umap-1.png" but not available.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Contains 2 files.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-01-11 12:25:28] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] HTTP 200
[2024-01-11 12:25:28] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:28] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from lines 78-80 [progeny] (pw_sc.Rmd)
Error: processing vignette 'pw_sc.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 ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Contains 2 files.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-01-11 12:25:31] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-01-11 12:25:31] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] HTTP 200
[2024-01-11 12:25:31] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:31] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from lines 109-111 [collectri] (tf_bk.Rmd)
Error: processing vignette 'tf_bk.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 ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
The magick package is required to crop "/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck/vign_test/decoupleR/vignettes/tf_sc_files/figure-html/umap-1.png" but not available.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Contains 2 files.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.17/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-01-11 12:25:36] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-01-11 12:25:36] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] HTTP 200
[2024-01-11 12:25:36] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 12:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-01-11 12:25:36] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.

Quitting from lines 86-88 [collectri] (tf_sc.Rmd)
Error: processing vignette 'tf_sc.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 ‘tf_sc.Rmd’

SUMMARY: processing the following files failed:
  ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.17/2024-01-11_1203/decoupleR/decoupleR.Rcheck/00check.log’
for details.

[ Finished: 2024-01-11 12:25:39 CET ]