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

To the developers/maintainers of the wppi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.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: wppi

Version: 1.15.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.15.0.tar.gz

StartedAt: 2025-01-22 12:33:22 -0000 (Wed, 22 Jan 2025)

EndedAt: 2025-01-22 12:44:40 -0000 (Wed, 22 Jan 2025)

EllapsedTime: 678.5 seconds

RetCode: 1

Status: ERROR

CheckDir: wppi.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.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 ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.15.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wppi’ 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/wppi.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 12:33:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:33:46] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:33:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:33:46] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 12:33:46] [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 12:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:33:46] [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 12:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:33:46] [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 12:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:33:46] [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 12:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:33:46] [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 12:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:05] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:34:05] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 12:34:05] [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 12:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:05] [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 12:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:06] [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 12:34:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:06] [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 12:34:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:06] [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 12:34:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:27] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-22 12:34:27] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-22 12:34:27] [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 12:34:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:28] [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 12:34:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:28] [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 12:34:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:28] [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 12:34:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:34:28] [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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘wppi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: common_neighbors
> ### Title: Shared neighbors of connected vertices
> ### Aliases: common_neighbors
> 
> ### ** Examples
> 
> graph_op <- graph_from_op(wppi_omnipath_data())
Warning in (function (...)  : 'function (...) 
{
    .Deprecated("post_translational")
    post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-01-22 12:35:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-01-22 12:35:04] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-22 12:35:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:35:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:35:04] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-22 12:35:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-22 12:35:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-22 12:35:04] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-22 12:35:04] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-22 12:35:04] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 12:35:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 12:38:08] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 12:38:08] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2025-01-22 12:38:13] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 12:41:15] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 12:41:15] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2025-01-22 12:41:20] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-22 12:44:35] [WARN]    [OmnipathR] HTTP 404
[2025-01-22 12:44:35] [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 in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 404
Backtrace:
     ▆
  1. ├─wppi::graph_from_op(wppi_omnipath_data())
  2. │ └─op_data %>% ...
  3. ├─dplyr::select(., -c(source_genesymbol, target_genesymbol))
  4. ├─wppi::wppi_omnipath_data()
  5. │ └─... %>% select(seq(10))
  6. ├─dplyr::select(., seq(10))
  7. ├─rlang::exec(., !!!omnipath_param)
  8. ├─OmnipathR (local) `<fn>`(entity_type = "protein")
  9. │ └─OmnipathR::post_translational(...)
 10. │   ├─rlang::exec(omnipath_query, !!!args)
 11. │   └─OmnipathR (local) `<fn>`(...)
 12. │     └─environment() %>% as.list %>% c(list(...)) %>% ...
 13. ├─OmnipathR:::omnipath_check_param(.)
 14. │ └─param$organisms %<>% map_int(ncbi_taxid)
 15. ├─purrr::map_int(., ncbi_taxid)
 16. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 17. │   ├─purrr:::with_indexed_errors(...)
 18. │   │ └─base::withCallingHandlers(...)
 19. │   ├─purrr:::call_with_cleanup(...)
 20. │   └─OmnipathR (local) .f(.x[[i]], ...)
 21. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 22. ├─purrr::map_int(., taxon_name, "ncbi")
 23. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 24. │   ├─purrr:::with_indexed_errors(...)
 25. │   │ └─base::withCallingHandlers(...)
 26. │   ├─purrr:::call_with_cleanup(...)
 27. │   └─OmnipathR (local) .f(.x[[i]], ...)
 28. │     ├─... %>% if_null_len0(NA)
 29. │     └─OmnipathR::get_db("organisms")
 30. │       └─OmnipathR::load_db(key, param = param)
 31. │         ├─rlang::exec(loader, !!!param)
 32. │         └─OmnipathR (local) `<fn>`()
 33. │           ├─... %>% ...
 34. │           └─OmnipathR::ensembl_organisms()
 35. │             ├─... %>% ...
 36. │             └─OmnipathR::ensembl_organisms_raw()
 37. │               └─... %>% html_table()
 38. ├─OmnipathR:::if_null_len0(., NA)
 39. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 40. ├─OmnipathR:::is_empty_2(.)
 41. │ └─value %>% ...
 42. ├─dplyr::first(.)
 43. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 44. │   └─vctrs::vec_size(x)
 45. ├─dplyr::pull(., name_type)
 46. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 47. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 48. ├─dplyr::mutate(...)
 49. ├─dplyr::full_join(...)
 50. ├─dplyr::mutate(...)
 51. ├─dplyr::select(...)
 52. ├─rvest::html_table(.)
 53. ├─rvest::html_element(., "table")
 54. ├─xml2::read_html(.)
 55. ├─OmnipathR:::download_to_cache(., req_headers = user_agent())
 56. │ └─OmnipathR:::download_base(...)
 57. │   └─base::stop(result)
 58. └─purrr (local) `<fn>`(`<smplErrr>`)
 59.   └─cli::cli_abort(...)
 60.     └─rlang::abort(...)
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: 1 ERROR, 5 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:05] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-21 20:10:05] [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 20:10:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:05] [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 20:10:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:05] [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 20:10:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:05] [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 20:10:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:05] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** 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 20:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:10] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:10] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-21 20:10:10] [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 20:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:10] [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 20:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:10] [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 20:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:10] [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 20:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:10] [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 20:10:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:15] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-21 20:10:15] [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 20:10:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:15] [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 20:10:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:15] [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 20:10:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:15] [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 20:10:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 20:10:15] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

Tests output

Example timings

wppi.Rcheck/wppi-Ex.timings

name

user

system

elapsed