NEWS.md
In FastRet: Retention Time Prediction in Liquid Chromatography

FastRet 1.1.3

Fixed issues mentioned by CRAN reviewer after initial submission of FastRet (v1.1.2):
- Comment 1: Please do not modify the .GlobalEnv. This is not allowed by the CRAN policies. -> R/patch.R
- Solution: 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.
- Comment 2: Please add \value to .Rd files regarding exported methods and explain the functions' results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, document that too, e.g., \value{No return value, called for side effects} or similar) -> Missing Rd-tags: adjust_frm.Rd: \value, analyzeCDNames.Rd: \value, getCDs.Rd: \value, getCDsFor1Molecule.Rd: \value, read_rpadj_xlsx.Rd: \value
- Solution: Added \value tags to the mentioned .Rd files describing the functions' return values.
- Comment 3: If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form authors (year) authors (year, ISBN:...) or if those are not available: with no space after 'doi:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")
- Solution: Added Bonini et al. (2020) 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

Added RAM caching to getCDs()

FastRet 1.0.3

Initial CRAN Submission.

Rejected because the following examples caused at least one of the following notes on the CRAN testing machines: CPU time > 5s, 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 |