[ Started: 2023-01-26 01:23:11 CET ]
[ OmnipathR v3.6.0 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ]

* using log directory ‘/home/omnipath/testing/bioc/omnipathr/bioc-3.16/2023-01-26_0117/OmnipathR/OmnipathR.Rcheck’
* using R version 4.2.2 Patched (2022-11-10 r83330)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.6.0’
* 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 ‘OmnipathR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2023-01-26 01:23:35] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-01-26 01:23:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-01-26 01:23:35] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-01-26 01:23:35] [TRACE]   [OmnipathR] Contains 1 files.
[2023-01-26 01:23:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-01-26 01:23:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-01-26 01:23:35] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-01-26 01:23:35] [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: harmonizome_download
> ### Title: Downloads a Harmonizome network dataset
> ### Aliases: harmonizome_download
> 
> ### ** Examples
> 
> harmonizome_data <- harmonizome_download('phosphositeplus')
[2023-01-26 01:28:49] [INFO]    [OmnipathR] Looking up in cache `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz`: key=ec4187d2e3f788b67450a4af5586d74c65db7687, no version available.
[2023-01-26 01:28:49] [INFO]    [OmnipathR] Created new version for cache record ec4187d2e3f788b67450a4af5586d74c65db7687: version 1.
[2023-01-26 01:28:49] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/ec4187d2e3f788b67450a4af5586d74c65db7687-1.gz
[2023-01-26 01:28:49] [INFO]    [OmnipathR] Retrieving URL: `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz`
[2023-01-26 01:28:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz`
[2023-01-26 01:31:50] [WARN]    [OmnipathR] HTTP 504
[2023-01-26 01:31:50] [WARN]    [OmnipathR] Failed to download `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz` (attempt 1/3); error: HTTP 504
[2023-01-26 01:31:55] [TRACE]   [OmnipathR] Attempt 2/3: `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz`
[2023-01-26 01:34:55] [WARN]    [OmnipathR] HTTP 504
[2023-01-26 01:34:55] [WARN]    [OmnipathR] Failed to download `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz` (attempt 2/3); error: HTTP 504
[2023-01-26 01:35:00] [TRACE]   [OmnipathR] Attempt 3/3: `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz`
[2023-01-26 01:37:00] [WARN]    [OmnipathR] HTTP 504
[2023-01-26 01:37:00] [ERROR]   [OmnipathR] Failed to download `https://maayanlab.cloud/static/hdfs/harmonizome/data/phosphositeplus/gene_attribute_edges.txt.gz` (attempt 3/3); error: HTTP 504
Error in (function (url, post = NULL, ...)  : HTTP 504
Calls: harmonizome_download -> download_to_cache -> download_base
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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘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
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/omnipath/testing/bioc/omnipathr/bioc-3.16/2023-01-26_0117/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2023-01-26 01:42:37 CET ]