Michael R. Crusoe pushed to branch debian/experimental at Debian Med / hisat2
Commits: 4ef97c9b by Michael R. Crusoe at 2021-01-27T16:55:24+01:00 debian/patches/riscv5: fix compilation on riscv5 - - - - - b3a001b6 by Michael R. Crusoe at 2021-01-27T17:34:03+01:00 routine-update: Standards-Version: 4.5.1 - - - - - 5c4b14b9 by Michael R. Crusoe at 2021-01-27T17:34:32+01:00 routine-update: Ready to upload to unstable - - - - - 455ae199 by Andreas Tille at 2021-09-28T10:28:28+02:00 routine-update: Fix watchfile to detect new versions on github - - - - - 0c76c9e0 by Andreas Tille at 2021-09-28T10:28:42+02:00 routine-update: Standards-Version: 4.6.0 - - - - - 5a11279e by Andreas Tille at 2021-09-28T10:35:37+02:00 Fix debian/source/lintian-overrides - - - - - a49e9e4c by Andreas Tille at 2021-09-28T10:38:50+02:00 Upload to unstable - - - - - 877371e5 by Andreas Tille at 2022-10-14T18:55:00+02:00 Fix watch file - - - - - 25015d77 by Andreas Tille at 2022-10-14T18:55:31+02:00 routine-update: Standards-Version: 4.6.1 - - - - - e2a7d4f0 by Andreas Tille at 2022-10-14T20:18:21+02:00 Update lintian-overrides - - - - - 06425a54 by Andreas Tille at 2022-10-14T20:22:59+02:00 Upload to unstable - - - - - 391f07ca by Michael R. Crusoe at 2023-01-22T18:03:28+01:00 Experimental rebuild with SIMDe 0.7.3~0git20230118123246.d1e75cd - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/riscv5 - debian/patches/series - debian/source/lintian-overrides - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,34 @@ +hisat2 (2.2.1-5~0exp) experimental; urgency=medium + + * Experimental rebuild with SIMDe 0.7.3~0git20230118123246.d1e75cd + + -- Michael R. Crusoe <[email protected]> Sun, 22 Jan 2023 18:01:28 +0100 + +hisat2 (2.2.1-4) unstable; urgency=medium + + * Team upload + * Fix watch file + * Standards-Version: 4.6.1 (routine-update) + * Update lintian-overrides + + -- Andreas Tille <[email protected]> Fri, 14 Oct 2022 20:18:28 +0200 + +hisat2 (2.2.1-3) unstable; urgency=medium + + * Team upload. + * Fix watchfile to detect new versions on github (routine-update) + * Standards-Version: 4.6.0 (routine-update) + * Fix debian/source/lintian-overrides + + -- Andreas Tille <[email protected]> Tue, 28 Sep 2021 10:35:43 +0200 + +hisat2 (2.2.1-2) unstable; urgency=medium + + * debian/patches/riscv5: fix compilation on riscv5 + * Standards-Version: 4.5.1 (routine-update) + + -- Michael R. Crusoe <[email protected]> Wed, 27 Jan 2021 17:34:32 +0100 + hisat2 (2.2.1-1) unstable; urgency=medium [ Steffen Moeller ] ===================================== debian/control ===================================== @@ -4,11 +4,11 @@ Uploaders: Michael R. Crusoe <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 13), - libsimde-dev, + libsimde-dev (>= 0.7.3~0git20230118123246.d1e75cd), help2man <!nodoc>, pandoc <!nodoc>, python3:any <!nodoc> -Standards-Version: 4.5.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/hisat2 Vcs-Git: https://salsa.debian.org/med-team/hisat2.git Homepage: https://daehwankimlab.github.io/hisat2/ ===================================== debian/patches/riscv5 ===================================== @@ -0,0 +1,35 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Fix compilation on riscv5 +--- hisat2.orig/alphabet.cpp ++++ hisat2/alphabet.cpp +@@ -400,7 +400,7 @@ + + const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn"; + +-char mask2iupac[16] = { ++int mask2iupac[16] = { + -1, + 'A', // 0001 + 'C', // 0010 +--- hisat2.orig/alphabet.h ++++ hisat2/alphabet.h +@@ -65,7 +65,7 @@ + /// corresponding 2-bit nucleotide + extern uint8_t nuccol2nuc[5][5]; + /// Convert a 4-bit mask into an IUPAC code +-extern char mask2iupac[16]; ++extern int mask2iupac[16]; + + /// Convert an ascii color to an ascii dna char + extern char col2dna[]; +--- hisat2.orig/sstring.h ++++ hisat2/sstring.h +@@ -3326,7 +3326,7 @@ + */ + char toChar(size_t idx) const { + assert_range((int)this->cs_[idx], 0, 15); +- return mask2iupac[(int)this->cs_[idx]]; ++ return (char)mask2iupac[(int)this->cs_[idx]]; + } + + /** ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ compilerflags simde python3 fix-manual +riscv5 ===================================== debian/source/lintian-overrides ===================================== @@ -1,2 +1,3 @@ # normal HTML -hisat2 source: source-is-missing docs/_includes/share-buttons.html line length is 278 characters (>256) +hisat2 source: source-is-missing [docs/_includes/share-buttons.html] +hisat2 source: source-is-missing [docs_jhu/manual.inc.html] ===================================== debian/watch ===================================== @@ -1,4 +1,4 @@ version=4 opts="filenamemangle=s%(?:.*?)?v(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \ - https://github.com/DaehwanKimLab/hisat2/releases .*/archive/v@ANY_VERSION@\.tar\.gz + https://github.com/DaehwanKimLab/hisat2/tags .*/v@ANY_VERSION@\.tar\.gz View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/d6499b1debf00393658631c0b71edab12cff26dd...391f07cac26cfbb416d71671bc88316b62aa4310 -- View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/d6499b1debf00393658631c0b71edab12cff26dd...391f07cac26cfbb416d71671bc88316b62aa4310 You're receiving this email because of your account on salsa.debian.org.
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