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qtl

ANALYTICS
Velocity0.0

Tools for Analyzing QTL Experiments

github.com/kbroman/qtl ↗

R/qtl is in pure custodial mode: every recent release answers a compiler, not a user

geneticsqtl-mappingstatistical-genomicsr-packagemaintenance
◆Current state
R/qtl is the long-established R package for QTL mapping in experimental crosses, covering interval mapping, composite interval mapping, multiple-QTL model fitting and the associated cross data formats. Nothing in the recent release history adds capability. Version 1.74 removes an include that started warning on CRAN, 1.72 improves an error message in cim(), and 1.70 migrates the C code from Calloc/Realloc/Free to their R_-prefixed equivalents for R-devel.
◆Where it's heading
The package is being maintained, not developed. The work divides cleanly into keeping the compiled code building against successive R and toolchain versions, and fixing narrow bugs reported through the issue tracker. The C-level migrations in particular are compliance with R's tightening of its C interface rather than anything chosen. Users should read the stability as maturity: the analysis surface has been fixed for years and the maintainer is keeping it installable.
◆Prediction
R has continued to restrict its non-API C entry points, and this package has already made two such migrations, so further compile-time compliance work is the most likely content of the next release.

◆Recent moves

  1. 8mo ago

    Remove R_ext/PrtUtil.h include flagged by CRAN

    Drops an include that had begun producing CRAN warnings. Compile-time hygiene, continuing the same C-interface compliance thread as 1.70.

    View source ↗
  2. 8mo ago

    Clearer cim() error when multiple phenotypes are passed

    Improves the error message and help text for cim() when more than one pheno.col is supplied, emphasising that only a single phenotype is supported. Diagnostics only; the restriction itself is unchanged.

    View source ↗
  3. 1y ago

    C memory calls migrated to R_Calloc/R_Realloc/R_Free

    Migrates simulate.c to the R_-prefixed memory macros and switches mqmdatatypes.cpp to Rf_warning() for R-devel compatibility, plus a help file typo and an Authors@R field. Entirely toolchain-driven.

    View source ↗
  4. 2y ago

    Fix Rprintf call and remaining compiler warnings

    Corrects an Rprintf call in C++ identified by CRAN and clears further compiler warnings. No change to analysis behaviour.

    View source ↗
  5. 2y ago

    Fix summary.scanone() thresholds and csvs phenotype reading

    Fixes summary.scanone() when format is onepheno and threshold has length greater than one, and read.cross() for csvs files whose phenotype file contains only identifiers. Two narrow edge cases from the issue tracker.

    View source ↗
  6. 3y ago

    Fix addint()/addcovarint() with X chromosome QTL and missing phenotypes

    Fixes an error in addint() and addcovarint() when an X chromosome QTL met missing phenotypes and the cross was not being subset, and modernises the CITATION file. Bug fix in an interaction-testing edge case.

    View source ↗