Multiple platform build/check report for BioC 3.21 - CHECK results for OmnipathR on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4779
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4503
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4468
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4423
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4407
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for OmnipathR on kunpeng2

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: OmnipathR

Version: 3.15.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.15.0.tar.gz

StartedAt: 2025-01-22 09:36:14 -0000 (Wed, 22 Jan 2025)

EndedAt: 2025-01-22 09:56:40 -0000 (Wed, 22 Jan 2025)

EllapsedTime: 1226.3 seconds

RetCode: 1

Status: ERROR

CheckDir: OmnipathR.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:31] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:32] [TRACE]   [OmnipathR] Cache locked: FALSE

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-22 09:36:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:36:44] [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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:01] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: all_uniprots
> ### Title: A table with all UniProt records
> ### Aliases: all_uniprots
> 
> ### ** Examples
> 
> human_swissprot_entries <- all_uniprots(fields = 'id')
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-22 09:37:43] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:37:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:40:46] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 09:40:46] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2025-01-22 09:40:51] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:43:53] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 09:43:53] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2025-01-22 09:43:58] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 09:47:00] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 09:47:00] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
Error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 404
Backtrace:
     ▆
  1. ├─OmnipathR::all_uniprots(fields = "id")
  2. │ └─organism %<>% ncbi_taxid
  3. ├─OmnipathR::ncbi_taxid(.)
  4. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
  5. ├─purrr::map_int(., taxon_name, "ncbi")
  6. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
  7. │   ├─purrr:::with_indexed_errors(...)
  8. │   │ └─base::withCallingHandlers(...)
  9. │   ├─purrr:::call_with_cleanup(...)
 10. │   └─OmnipathR (local) .f(.x[[i]], ...)
 11. │     ├─... %>% if_null_len0(NA)
 12. │     └─OmnipathR::get_db("organisms")
 13. │       └─OmnipathR::load_db(key, param = param)
 14. │         ├─rlang::exec(loader, !!!param)
 15. │         └─OmnipathR (local) `<fn>`()
 16. │           ├─... %>% ...
 17. │           └─OmnipathR::ensembl_organisms()
 18. │             ├─... %>% ...
 19. │             └─OmnipathR::ensembl_organisms_raw()
 20. │               └─... %>% html_table()
 21. ├─OmnipathR:::if_null_len0(., NA)
 22. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 23. ├─OmnipathR:::is_empty_2(.)
 24. │ └─value %>% ...
 25. ├─dplyr::first(.)
 26. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 27. │   └─vctrs::vec_size(x)
 28. ├─dplyr::pull(., name_type)
 29. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 30. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 31. ├─dplyr::mutate(...)
 32. ├─dplyr::full_join(...)
 33. ├─dplyr::mutate(...)
 34. ├─dplyr::select(...)
 35. ├─rvest::html_table(.)
 36. ├─rvest::html_element(., "table")
 37. ├─xml2::read_html(.)
 38. ├─OmnipathR:::download_to_cache(., req_headers = user_agent())
 39. │ └─OmnipathR:::download_base(...)
 40. │   └─base::stop(result)
 41. └─purrr (local) `<fn>`(`<smplErrr>`)
 42.   └─cli::cli_abort(...)
 43.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Caused by error in `map_int()`:
  ℹ In index: 1.
  Caused by error:
  ! HTTP 404
  Class:   purrr_error_indexed/rlang_error/error/condition
  ── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ─────────
  Error in `eval(code, test_env)`: object 'response' not found
  Backtrace:
      ▆
   1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13
   2. └─tidyr::separate_rows(., sources, sep = ";")
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 5 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:55] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Contains 4 files.
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-21 20:09:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-21 20:09:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-21 20:09:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-21 20:09:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:56] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-21 20:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-21 20:09:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-21 20:09:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:09:59] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout.fail


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> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
Warning: program compiled against libxml 212 using older 211
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:47:07] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Contains 2 files.
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:47:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 09:47:07] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_import.R:169:9'): Testing `complexes` ────────────────────────
`assign("response", method(resources = resources), envir = top_env)` threw an error.
Message: ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 404
Class:   purrr_error_indexed/rlang_error/error/condition
── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ─────────
Error in `eval(code, test_env)`: object 'response' not found
Backtrace:
    ▆
 1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13
 2. └─tidyr::separate_rows(., sources, sep = ";")

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

name	user	system	elapsed
OmnipathR	0	0	0
all_uniprot_acs	0.027	0.000	0.027