LoginSign Up
← Back to all sparks
M

mpactr

INFRA · APIS
Velocity0.0

Correction of Preprocessed MS Data

github.com/mums2/mpactr ↗

mpactr spent two spring releases normalizing case in metadata after users kept tripping on it.

metabolomicsmass-spectrometrypeak-filteringdata-importr-packages
◆Current state
mpactr filters mass-spectrometry peak tables — removing contaminants, ion duplicates and low-reproducibility features before downstream metabolomics analysis — with a data.table and Rcpp core. Development is slow and the recent releases are small. The May pair both address the same friction: column names and imported table names arriving in inconsistent case and failing to match.
◆Where it's heading
The package is stabilizing its input contract rather than growing its filtering methods. Metadata column names are now forced lowercase inside import_data() regardless of how the file was written, imported peak_tables names not present in the injection column are lowercased too, and get_meta_data() was renamed to get_metadata() in the same pass. Before that the work was infrastructural — Rcpp introduced to speed up filtering, data.table moved from Depends to Imports, and memory errors cleared so the package passes Valgrind and both sanitizers. Note the earliest entry compares against a v1.0.0 tag that precedes 0.1.0 in the repository, so version ordering in this feed is not reliable.
◆Prediction
The case-normalization work has now touched both metadata columns and peak table names across two consecutive releases, which suggests the input-matching problem is not fully closed and a third pass is plausible. Nothing in these entries points to new filtering methods.

◆Recent moves

  1. 3mo ago

    Peak table names lowercased when absent from the injection column

    A follow-on to the previous release's case normalization, extending it from metadata columns to imported peak_tables names. Internal naming consistency with no change to filtering behaviour.

    View source ↗
  2. 3mo ago

    Metadata column names forced lowercase; get_metadata() renamed

    Fixes the input contract at its source: import_data() now lowercases every metadata column name, so files written with uppercase headers stop failing to match. The get_meta_data() to get_metadata() rename breaks existing calls, which is the part users have to act on.

    View source ↗
  3. 10mo ago

    Valgrind and sanitizer memory issues cleared

    Compiled-code hygiene so the package passes under Valgrind, clang-asan and gcc-asan, plus a limit_cores() helper for CRAN check environments. Invisible to users, necessary for the compiled filtering path to stay on CRAN.

    View source ↗
  4. 1y ago

    Rcpp added to speed up filtering; data.table moved to Imports

    The performance foundation of the package as it stands — filtering moves into compiled code — with data.table demoted from Depends to Imports so it no longer attaches to the user's search path. A duplication error is fixed alongside.

    View source ↗
  5. 1y ago

    mpactr 0.1.0

    A pull-request pointer with no description of what changed. Its changelog link compares from a v1.0.0 tag to 0.1.0, which is the clearest sign that tag ordering in this repository does not follow version order.

    View source ↗