CVS commit: pkgsrc/biology/htslib

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Oct 11 22:36:15 UTC 2024

Modified Files:
        pkgsrc/biology/htslib: Makefile PLIST buildlink3.mk distinfo

Log Message:
biology/htslib: Update to 1.21

Numerous bug fixes and enhancements since 1.17
Changes:        https://github.com/samtools/htslib/releases

Reported by:    portscout


To generate a diff of this commit:
cvs rdiff -u -r1.37 -r1.38 pkgsrc/biology/htslib/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/htslib/PLIST
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/htslib/buildlink3.mk
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/htslib/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/htslib/Makefile
diff -u pkgsrc/biology/htslib/Makefile:1.37 pkgsrc/biology/htslib/Makefile:1.38
--- pkgsrc/biology/htslib/Makefile:1.37 Sun Jul  7 09:51:44 2024
+++ pkgsrc/biology/htslib/Makefile      Fri Oct 11 22:36:15 2024
@@ -1,7 +1,8 @@
-# $NetBSD: Makefile,v 1.37 2024/07/07 09:51:44 nia Exp $
+# $NetBSD: Makefile,v 1.38 2024/10/11 22:36:15 bacon Exp $
 
-DISTNAME=      htslib-1.17
-PKGREVISION=   5
+# CAUTION: htslib should always be upgraded in conjunction with
+# samtools, bcftools, bio-mocha, and bcf-score
+DISTNAME=      htslib-1.21
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
 GITHUB_RELEASE=        ${PKGVERSION_NOREV}
@@ -12,17 +13,13 @@ HOMEPAGE=   https://www.htslib.org/
 COMMENT=       C library for high-throughput sequencing data formats
 LICENSE=       mit
 
-USE_TOOLS+=            autoconf automake autoreconf bash gmake perl
+USE_TOOLS+=            autoconf automake autoreconf bash:test gmake perl:test
 GNU_CONFIGURE=         yes
 CONFIGURE_ARGS+=       --enable-libcurl
 PKGCONFIG_OVERRIDE=    htslib.pc.in
 TEST_TARGET=           test
 MAKE_ENV+=             BUILT_TEST_PROGRAMS=''
 
-# Causes build failures:
-# error: incompatible type for argument 1 of 'vreinterpret_u16_u8'
-CONFIGURE_ENV.NetBSD+= hts_cv_have_neon=no
-
 SUBST_CLASSES+=                version
 SUBST_STAGE.version=   pre-configure
 SUBST_SED.version=     -e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
@@ -36,5 +33,7 @@ pre-configure:
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../archivers/xz/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/libdeflate/buildlink3.mk"
+.include "../../security/openssl/buildlink3.mk"
 .include "../../www/curl/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/htslib/PLIST
diff -u pkgsrc/biology/htslib/PLIST:1.6 pkgsrc/biology/htslib/PLIST:1.7
--- pkgsrc/biology/htslib/PLIST:1.6     Sat Feb 25 13:50:38 2023
+++ pkgsrc/biology/htslib/PLIST Fri Oct 11 22:36:15 2024
@@ -1,4 +1,5 @@
-@comment $NetBSD: PLIST,v 1.6 2023/02/25 13:50:38 bacon Exp $
+@comment $NetBSD: PLIST,v 1.7 2024/10/11 22:36:15 bacon Exp $
+bin/annot-tsv
 bin/bgzip
 bin/htsfile
 bin/tabix
@@ -35,6 +36,7 @@ lib/libhts.so
 lib/libhts.so.${PKGVERSION}
 lib/libhts.so.3
 lib/pkgconfig/htslib.pc
+man/man1/annot-tsv.1
 man/man1/bgzip.1
 man/man1/htsfile.1
 man/man1/tabix.1

Index: pkgsrc/biology/htslib/buildlink3.mk
diff -u pkgsrc/biology/htslib/buildlink3.mk:1.9 pkgsrc/biology/htslib/buildlink3.mk:1.10
--- pkgsrc/biology/htslib/buildlink3.mk:1.9     Sat Feb 25 13:50:38 2023
+++ pkgsrc/biology/htslib/buildlink3.mk Fri Oct 11 22:36:15 2024
@@ -1,12 +1,12 @@
-# $NetBSD: buildlink3.mk,v 1.9 2023/02/25 13:50:38 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.10 2024/10/11 22:36:15 bacon Exp $
 
 BUILDLINK_TREE+=       htslib
 
 .if !defined(HTSLIB_BUILDLINK3_MK)
 HTSLIB_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.htslib+= htslib>=1.17
-BUILDLINK_ABI_DEPENDS.htslib+= htslib>=1.17
+BUILDLINK_API_DEPENDS.htslib+= htslib>=1.21
+BUILDLINK_ABI_DEPENDS.htslib+= htslib>=1.21
 BUILDLINK_PKGSRCDIR.htslib?=   ../../biology/htslib
 
 .endif # HTSLIB_BUILDLINK3_MK

Index: pkgsrc/biology/htslib/distinfo
diff -u pkgsrc/biology/htslib/distinfo:1.11 pkgsrc/biology/htslib/distinfo:1.12
--- pkgsrc/biology/htslib/distinfo:1.11 Sat Feb 25 13:50:38 2023
+++ pkgsrc/biology/htslib/distinfo      Fri Oct 11 22:36:15 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.11 2023/02/25 13:50:38 bacon Exp $
+$NetBSD: distinfo,v 1.12 2024/10/11 22:36:15 bacon Exp $
 
-BLAKE2s (htslib-1.17.tar.bz2) = 01a90e639179c0f819a24f74cfe232963699c79b94c153e45f23a2bccac50373
-SHA512 (htslib-1.17.tar.bz2) = 624ab449d57713dab2d34399926c065f8cff8a45e6fbe68e0bb518c601421f587b613caeb095f8639b1d67cdb4a65d658c85f942173bcaa48da026fe15def5d3
-Size (htslib-1.17.tar.bz2) = 4619884 bytes
+BLAKE2s (htslib-1.21.tar.bz2) = 56d6dde2945d162fda083d1d3a79aab5fb0bfce2c9e3538db46367d4953a69ff
+SHA512 (htslib-1.21.tar.bz2) = 4989d9fd3702893d2b275e6de593a2109a0ebd10c0329ddca82cd3d53893a93197b9ca9f3756c480c88dc345e14527b1a540810089a480d839814e018a736bee
+Size (htslib-1.21.tar.bz2) = 4781943 bytes