[ Started: 2023-02-09 02:05:54 CET ]
[ wppi v1.6.0 for BioC-3.16 from https://github.com/AnaGalhoz37/wppi@main ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:01] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Contains 1 files.
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-09 02:06:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-02-09 02:06:02] [INFO]    [wppi] Executing WPPI workflow.
[2023-02-09 02:06:02] [INFO]    [wppi] Collecting database knowledge.
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-02-09 02:06:02] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:02] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-02-09 02:06:02] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-09 02:06:02] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2023-02-09 02:06:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2023-02-09 02:06:06] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2023-02-09 02:06:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-09 02:06:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-02-09 02:06:06] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
Quitting from lines 80-102 (wppi_workflow.Rmd) 
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
ℹ In argument: `across(everything(), na_if, "-")`.
Caused by error in `across()`:
! Can't compute column `entrez_gene_id`.
Caused by error in `fn()`:
! Can't convert `y` <character> to match type of `x` <double>.
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2023-02-09 02:06:06 CET ]