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Changelog

Source: NEWS.md

FastRet 1.1.5

  • Improved read_retip_hilic_data(): the dataset is now only downloaded from GitHub if the package is not installed. If it is installed, the dataset is loaded directly.

  • Internal Changes:

    • Removed TODOS.md
    • Bumped version to 1.1.5
    • Moved all data related functions from util.R to data.R
    • Added a README to misc/datasets
    • Added functions load_all() and document() to util.R
    • Replaced xlsx and readxl packages with openxlsx

FastRet 1.1.4

CRAN release: 2025-02-10

  • Added a cache cleanup handler that gets registered via reg.finalizer() upon package loading to ensure that the cache directory is removed if it doesn’t contain any files that should persist between R sessions.

  • Added an article about installation details incl. a troubleshooting section

  • Improved function docs

  • Improved examples by removing donttest blocks

  • Improved examples & tests by using smaller example datasets to reduce runtime

FastRet 1.1.3

CRAN release: 2024-06-25

  • Moved patch.R from the R folder to misc/scripts, which is excluded from the package build using .Rbuildignore. The file is conditionally sourced by the private function start_gui_in_devmode() if available, allowing its use during development without including it in the package.

  • Added \value tags to the mentioned .Rd files describing the functions’ return values.

  • Added Bonini et al. (2020) doi:10.1021/acs.analchem.9b05765 as reference to the description part of the DESCRIPTION file, listing it as Related work. This reference is used in the documentation for read_retip_hilic_data() and ram_cache. No additional references are used in the package documentation.

  • Added Fadi Fadil as a contributor. Fadi measured the example datasets shipped with FastRet.

  • Added ORCID IDs for contributors as described in CRAN’s checklist for submissions.

FastRet 1.1.2

  • Wrapped examples of read_rp_xlsx() and read_rpadj_xlsx() into donttest to prevent note “Examples with CPU time > 2.5 times elapsed time: …”. By now I’m pretty sure the culprit is the xlsx package, which uses a java process for reading the file. Maybe we should switch to openxlsx or readxl in the future.

FastRet 1.1.1

  • Improved examples of preprocess_data() to prevent note “Examples with CPU time > 2.5 times elapsed time: preprocess_data (CPU=2.772, elapsed=0.788)”.

FastRet 1.1.0

FastRet 1.0.3

  • Added examples to start_gui(), fastret_app(), getCDsFor1Molecule(), analyzeCDNames(), check_lm_suitabilitym(), plot_lm_suitability(), extendedTask(), selective_measuring(), train_frm(), adjust_frm(), get_predictors()

  • Improved lots of existing examples

  • Added additionalo logging messages at various places

  • Submitted to CRAN, but rejected because the following examples caused at least one of the following notes on the CRAN testing machines: (1) “CPU time > 5s”, (2) “CPU time > 2.5 times elapsed time”. In this context, “CPU time” is calculated as the sum of the measured “user” and “system” times.

    function user system elapsed ratio
    check_lm_suitability 5.667 0.248 2.211 2.675
    predict.frm 2.477 0.112 0.763 3.393
    getCDs 2.745 0.089 0.961 2.949

FastRet 1.0.2

  • Improved github actions

FastRet 1.0.1

  • Improved github actions

FastRet 1.0.0

Completely refactored source code, e.g.:

  • Added a test suite covering all important functions

  • The UI now uses Extended Tasks for background processing, allowing GUI usage by multiple users at the same time

  • The clustering now uses Partitioning Around Medoids (PAM) instead of k-means, which is faster and much better suited for our use case

  • The training of the Lasso and/or XGBoost models is no longer done using caret but using glmnet and xgboost directly. The new implementation is much faster and allows for full control over the number of workers started.

  • Function getCDs now caches the results on Disk, making the retrieval of chemical descriptors much faster

  • The GUI now has a console element, showing the progress of the background tasks like clustering and model training

  • The GUI has a cleaner interface, because lots of the options are now hidden in the “Advanced” tab by default and are only displayed upon user request

FastRet 0.99.7

  • Fixed R CMD check findings
  • Fixed Github Actions
  • Fixed Dockerfile

FastRet 0.99.6

  • Added contact, privacy policy
  • Fixed Dockerfile

FastRet 0.99.4

  • Improved Github Actions and Formatting of source code

FastRet 0.99.3

  • Reduce required R version in DESCRIPTION from 4.2 to 4.1
  • Added Dockerfile
  • Fixed R CMD check warnings
  • Fixed R CMD check action

FastRet 0.99.2

FastRet 0.99.1

  • Initial version.

    Copy of commit cd243aa82a56df405df8060b84535633cf06b692 of Christian Amesöders Repository. (Christian wrote this initial version of FastRet as part of his master thesis at the Institute of functional Genomics, University of Regensburg).