[ Started: 2024-05-19 15:49:55 CEST ]
[ OmnipathR v3.10.1 for BioC-3.18 from https://github.com/saezlab/OmnipathR@RELEASE_3_18 (b1b2bab 2023-10-25 17:47:10) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.10.1’
* 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  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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 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 startup messages can be suppressed ... NOTE
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:15] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-19 15:50:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:15] [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
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:21] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-19 15:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-19 15:50:21] [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 ... 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 ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... failed
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘bioc_workshop.Rmd’
  ...
[2024-05-19 15:57:45] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2024-05-19 15:57:45] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.

> uniprot_loc <- import_omnipath_annotations(resuorces = "UniProt_location", 
+     wide = TRUE)
[2024-05-19 15:57:45] [FATAL]   [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.

  When sourcing ‘bioc_workshop.R’:
Error: Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-19_1542/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2024-05-19 16:08:27 CEST ]