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fioRa

Mass-Spectra Prediction Using the FIORA Model

v0.3.7 · Jan 23, 2026 · MIT + file LICENSE
CRAN GitHub Mirror

Description

Provides a wrapper for the python module 'FIORA' as well as a 'shiny'-App to facilitate data processing and visualization. 'FIORA' allows to predict Mass-Spectra based on the SMILES code of chemical compounds. It is described in the Nature Communications article by Nowatzky (2025) <doi:10.1038/s41467-025-57422-4>.

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CRAN Check Status

4 ERROR
10 OK
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Flavor Status
r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc OK
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 OK
r-devel-windows-x86_64 ERROR
r-oldrel-macos-arm64 ERROR
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 ERROR
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 ERROR
r-release-windows-x86_64 OK
Check details (5 non-OK)
ERROR r-devel-windows-x86_64

tests

Running 'spelling.R' [0s]
  Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(fioRa)
  > 
  > testthat::test_check("fioRa")
  Saving _problems/test-fct_read_fiora-43.R
  Loading required package: shiny
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-app_utils.R:40:1', 'test-app_utils.R:66:1',
    'test-find_fiora_predict_paths.R:2:3', 'test-run_script.R:3:3',
    'test-run_script.R:18:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fct_read_fiora.R:43:3'): fioRa can read the standard fiora example annotated output mgf as Spectra format ──
  Error in `verify_suggested(pkg = c("S4Vectors", "Spectra"))`: The use of this function requires package Spectra. Please install.
  Backtrace:
      ▆
   1. └─fioRa::read_fiora(fl = fl, fmt = "Spectra") at test-fct_read_fiora.R:43:3
   2.   └─fioRa:::convert2Spectra(out)
   3.     └─fioRa:::verify_suggested(pkg = c("S4Vectors", "Spectra"))
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  Error:
  ! Test failures.
  Execution halted
NOTE r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘Spectra’
ERROR r-oldrel-macos-arm64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [10s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(fioRa)
  > 
  > testthat::test_check("fioRa")
  2026-03-23 08:13:39.564 R[89534:273587] XType: Using static font registry.
  Saving _problems/test-fct_read_fiora-43.R
  Loading required package: shiny
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-app_utils.R:40:1', 'test-app_utils.R:66:1',
    'test-find_fiora_predict_paths.R:2:3', 'test-run_script.R:3:3',
    'test-run_script.R:18:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fct_read_fiora.R:43:3'): fioRa can read the standard fiora example annotated output mgf as Spectra format ──
  Error in `verify_suggested(pkg = c("S4Vectors", "Spectra"))`: The use of this function requires package Spectra. Please install.
  Backtrace:
      ▆
   1. └─fioRa::read_fiora(fl = fl, fmt = "Spectra") at test-fct_read_fiora.R:43:3
   2.   └─fioRa:::convert2Spectra(out)
   3.     └─fioRa:::verify_suggested(pkg = c("S4Vectors", "Spectra"))
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  Error:
  ! Test failures.
  Downloading uv...Done!
  Downloading cpython-3.12.13-macos-aarch64-none (download) (16.8MiB)
   Downloaded cpython-3.12.13-macos-aarch64-none (download)
  Downloading numpy (14.0MiB)
   Downloaded numpy
  Installed 1 package in 10ms
  Execution halted
ERROR r-patched-linux-x86_64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [44s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(fioRa)
  > 
  > testthat::test_check("fioRa")
  Loading required package: shiny
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 47 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-app_utils.R:40:1', 'test-app_utils.R:66:1',
    'test-find_fiora_predict_paths.R:2:3', 'test-run_script.R:3:3',
    'test-run_script.R:18:3'
  
  [ FAIL 0 | WARN 0 | SKIP 5 | PASS 47 ]
  Error: /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /home/hornik/tmp/scratch/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
  Execution halted
ERROR r-release-macos-x86_64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [30s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(fioRa)
  > 
  > testthat::test_check("fioRa")
  Saving _problems/test-fct_read_fiora-43.R
  Loading required package: shiny
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-app_utils.R:40:1', 'test-app_utils.R:66:1',
    'test-find_fiora_predict_paths.R:2:3', 'test-run_script.R:3:3',
    'test-run_script.R:18:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fct_read_fiora.R:43:3'): fioRa can read the standard fiora example annotated output mgf as Spectra format ──
  Error in `verify_suggested(pkg = c("S4Vectors", "Spectra"))`: The use of this function requires package Spectra. Please install.
  Backtrace:
      ▆
   1. └─fioRa::read_fiora(fl = fl, fmt = "Spectra") at test-fct_read_fiora.R:43:3
   2.   └─fioRa:::convert2Spectra(out)
   3.     └─fioRa:::verify_suggested(pkg = c("S4Vectors", "Spectra"))
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  Error:
  ! Test failures.
  Execution halted

Check History

ERROR 10 OK · 0 NOTE · 0 WARNING · 4 ERROR · 0 FAILURE Mar 10, 2026
ERROR r-devel-linux-x86_64-debian-clang

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [44s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # 
...[truncated]...
ecution halted
  Warning message:
  Some Python package requirements declared via `py_require()` are not installed in the selected Python environment: (/home/hornik/tmp/scratch/check-CRAN-regular-hornik/.virtualenvs/r-reticulate/bin/python)
    numpy
ERROR r-devel-windows-x86_64

tests

Running 'spelling.R' [0s]
  Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where s
...[truncated]...
fl, fmt = "Spectra") at test-fct_read_fiora.R:43:3
   2.   └─fioRa:::convert2Spectra(out)
   3.     └─fioRa:::verify_suggested(pkg = c("S4Vectors", "Spectra"))
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-release-macos-x86_64

tests

Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [30s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # 
...[truncated]...
fl, fmt = "Spectra") at test-fct_read_fiora.R:43:3
   2.   └─fioRa:::convert2Spectra(out)
   3.     └─fioRa:::verify_suggested(pkg = c("S4Vectors", "Spectra"))
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 45 ]
  Error:
  ! Test failures.
  Execution halted
ERROR r-oldrel-macos-arm64

package dependencies

Package suggested but not available for checking: ‘Spectra’

Dependency Network

Dependencies Reverse dependencies bslib config golem InterpretMSSpectrum rcdk shiny shinyjs waiter fioRa

Version History

new 0.3.7 Mar 10, 2026
updated 0.3.7 ← 0.3.4 diff Jan 22, 2026
new 0.3.4 Nov 10, 2025