Michael R. Crusoe pushed to branch master at Debian Med / fermi-lite
Commits: bf6e08b6 by Michael R. Crusoe at 2020-03-30T10:33:09+02:00 fix sync_instead_of_atomic patch and re-enable it - - - - - c19499e7 by Michael R. Crusoe at 2020-03-30T10:49:48+02:00 Added a basic test - - - - - b4ea6f1d by Michael R. Crusoe at 2020-03-30T10:55:52+02:00 release 0.1-12 - - - - - 6 changed files: - debian/changelog - debian/patches/series - debian/patches/sync_instead_of_atomic - debian/rules - + debian/tests/asm - debian/tests/control Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +fermi-lite (0.1-12) unstable; urgency=medium + + * Team upload. + * debian/patches/sync_instead_of_atomic: fix logic and re-enable (fetch the + previous value, not the new one). Fixes build on mipsel. + * Added a basic package time test & autopkgtest to confirm the patch using + fml-asm + + -- Michael R. Crusoe <[email protected]> Mon, 30 Mar 2020 10:55:37 +0200 + fermi-lite (0.1-11) unstable; urgency=medium [ Steve Langasek ] ===================================== debian/patches/series ===================================== @@ -4,4 +4,4 @@ rename_bseq1_t.patch bcf_seqlib.patch simde ensure-signed-comparison.patch -# sync_instead_of_atomic +sync_instead_of_atomic ===================================== debian/patches/sync_instead_of_atomic ===================================== @@ -7,7 +7,7 @@ Subject: fix compatibility on mipsel uint64_t *p = bits + (x>>6); uint64_t z = 1LLU<<(x&0x3f); - __sync_fetch_and_or(p, z); -+ __atomic_or_fetch(p, z, __ATOMIC_SEQ_CST); ++ __atomic_fetch_or(p, z, __ATOMIC_SEQ_CST); } static inline void set_bits(uint64_t *bits, const rldintv_t *p) @@ -16,7 +16,7 @@ Subject: fix compatibility on mipsel p[0] = w->visited + (d->z.k[0]>>6); x[0] = 1LLU<<(d->z.k[0]&0x3f); p[1] = w->visited + (d->z.k[1]>>6); x[1] = 1LLU<<(d->z.k[1]&0x3f); - if ((__sync_fetch_and_or(p[0], x[0])&x[0]) || (__sync_fetch_and_or(p[1], x[1])&x[1])) return; -+ if ((__atomic_or_fetch(p[0], x[0], __ATOMIC_SEQ_CST)&x[0]) || (__atomic_or_fetch(p[1], x[1], __ATOMIC_SEQ_CST)&x[1])) return; ++ if ((__atomic_fetch_or(p[0], x[0], __ATOMIC_SEQ_CST)&x[0]) || (__atomic_fetch_or(p[1], x[1], __ATOMIC_SEQ_CST)&x[1])) return; d->z.len = d->str.l; if (d->max_l < d->str.m) { d->max_l = d->str.m; ===================================== debian/rules ===================================== @@ -35,3 +35,9 @@ override_dh_installman: -n 'assemble Illumina short reads in small regions' \ -N --no-discard-stderr -h '' ./fml-asm > fml-asm.1 dh_installman + +override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + ./fml-asm test/MT-simu.fq.gz > MT.fq + test "$$(wc -l < MT.fq)" = "4" +endif ===================================== debian/tests/asm ===================================== @@ -0,0 +1,8 @@ +#!/bin/sh +# autopkgtest check: confirm that fml-asm works +set -e + +INPUT=$(pwd)/test/MT-simu.fq.gz + +test "$(fml-asm ${INPUT} | wc -l)" = "4" +echo "run: OK" ===================================== debian/tests/control ===================================== @@ -1,3 +1,7 @@ Tests: build-lib Depends: @, build-essential Restrictions: allow-stderr + +Tests: asm +Depends: fml-asm +Restrictions: allow-stderr View it on GitLab: https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2 -- View it on GitLab: https://salsa.debian.org/med-team/fermi-lite/-/compare/e6ad3623bea78984a8c9013f027d29132008e2e6...b4ea6f1de4ad468a421fe67b44e661b6375488b2 You're receiving this email because of your account on salsa.debian.org.
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