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FracFixD v2.0.3 "Quokka-Static"

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@shnickol shnickol released this 27 May 05:44
· 9 commits to main since this release
fracfixd-v2.0.3
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FracFixD v2.0.3 "Quokka-Static" — 2026-05-27

Static-linkage fix release for the Linux GUI binaries.

No numeric-kernel changes from v2.0.2. Equivalence-harness
outputs are byte-identical to v2.0.2 on the synthetic and real-data
fixtures; the manuscript figures, the CLI default-flag output bytes
and the FFXD1BIN container layout all carry over unchanged.

Background

v2.0.2 shipped three Linux GUI binaries
(fracfixd-linux-{generic,broadwell,znver2}-x86_64) that were
mis-described in the release notes and the manuscript as
"statically linked". In fact they were dynamically linked against
the host's BLAS / LAPACK / gfortran / gomp stack, and would fail on
any Linux host without those system libraries installed. Affected
users saw, on launch:

./fracfixd-linux-<arch>-x86_64: error while loading shared libraries:
libopenblas.so.0: cannot open shared object file

Only the CLI-static variant (fracfixd-cli-linux-x86_64-static) was
genuinely statically linked.

What v2.0.3 fixes

All three Linux GUI binaries — and the CLI-static binary — are now
fully statically linked against OpenBLAS (with bundled netlib
LAPACK) and the gfortran / gomp / pthread runtimes. ldd on every
Linux release artefact now shows only:

linux-vdso.so.1, libm.so.6, libgcc_s.so.1, libc.so.6,
/lib64/ld-linux-x86-64.so.2

— the standard glibc system trio that cannot realistically be
statically linked on Linux. No libopenblas, liblapack,
libblas, libgfortran, libgomp or libquadmath references
remain in any DT_NEEDED entry.

GTK3 is loaded at runtime by the fracfixd gui subcommand via
dlopen and does not appear as a link-time dependency, matching
the v2.0.0 / v2.0.1 / v2.0.2 behaviour.

Verification

  • Static linkage: ldd per-binary confirmation; see "Linux
    binary downloads" below for SHA256SUMS.
  • Numerical regression: the equivalence harness
    (tests/equivalence/full/) was run against FracFixR 1.1.0
    (CRAN tarball) with both the v2.0.2 dynamic and v2.0.3 static
    CLI binaries on the same synthetic 1000-transcript fixture.
    Both binaries produced byte-identical d_diffprop_glm.tsv
    and d_diffprop_logit.tsv outputs (matching MD5). Static
    linkage is numerically transparent — it changes how OpenBLAS
    symbols are resolved (in-archive vs at runtime), not what they
    compute.
  • Per-microarch tuning preserved: each GUI variant compiled
    with --mcpu= set to znver2, broadwell, or x86-64-v3
    respectively, --flto=full, -O3, -boundscheck=off,
    matching the v2.0.2 microarch surface.

Linux binary downloads

File Microarch Size (stripped)
fracfixd-linux-znver2-x86_64 AMD Zen 2 (AVX2 + BMI2 tuned) 7.9 MB
fracfixd-linux-broadwell-x86_64 Intel Broadwell (AVX2) 8.0 MB
fracfixd-linux-generic-x86_64 x86-64-v3 (generic AVX2 baseline) 8.0 MB
fracfixd-cli-linux-x86_64-static x86-64-v2 (SSE4.2, CLI-only) 2.3 MB

See SHA256SUMS attached to this release.

macOS arm64 and Windows x86_64

The macOS arm64 .dmg / tarball and the Windows x86_64 portable
ZIP from v2.0.2 are not affected by this fix; they are carried
forward unchanged. Verify with otool -L on macOS and the
bundled OpenBLAS.dll on Windows.

Build provenance

  • Host: Manjaro Linux, AMD Ryzen 5 4600G, 30 GB RAM
  • Toolchain: LDC 1.42.0 (LLVM 21.1.8, DMD frontend 2.112.1)
  • OpenBLAS: v0.3.27 built with NO_SHARED=1 USE_THREAD=0 NUM_THREADS=1 DYNAMIC_ARCH=1 NO_AFFINITY=1 NO_WARMUP=1 NO_LAPACKE=1 BUILD_LAPACK_DEPRECATED=0 via
    scripts/build_static_openblas.sh
  • Build types: release-{znver2,broadwell,generic}-static (GUI)
    and release-cli-static-flto (CLI-only); see dub.json.

Carry-overs from v2.0.2

Everything from v2.0.2 stays in place:

  • Multi-condition diagnostic plot suite (global-test volcano,
    p-value histogram, per-contrast volcano grid, top-N heatmap)
  • FFXD1ICA fast-load cache for the 205k-row reference TSV
  • Determinate progress + working Cancel on long-running jobs
  • Ctrl-wheel / Ctrl-+/-/0 plot zoom
  • 360×240 window minimum + per-tab scrollbars on shrink
  • The full v2.0.0 statistical surface: seven differential-proportion
    test backends, three dispersion modes, three FDR procedures,
    three log₂ fold-change shrinkage estimators, permutation
    inference, Bayesian credible intervals, multi-condition global
    LRT / Wald.

Citation

If you use FracFixD in published work please cite:

  • the FracFixR method paper (Cleynen, Hauling & Shirokikh, 2026 —
    see the repository CITATION.cff), and
  • this release via its Zenodo concept DOI
    10.5281/zenodo.20234583
    or v2.0.3 version DOI (to be minted with this release).
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