kallisto: Bump PKGREVISION, clean up

[Jason Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Tue May 27 08:55:12 2025 -0500
Changeset:	27ebcbfb09b084827bc45faa3d934f8e6f515c4b

Modified Files:
	kallisto/DESCR
	kallisto/Makefile
	kallisto/distinfo
Added Files:
	kallisto/patches/patch-ext_bifrost_src_DataStorage.tcc

Log Message:
kallisto: Bump PKGREVISION, clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=27ebcbfb09b084827bc45faa3d934f8e6f515c4b

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

diffstat:
 kallisto/DESCR                                         |  9 +++++----
 kallisto/Makefile                                      |  5 +++--
 kallisto/distinfo                                      |  1 +
 kallisto/patches/patch-ext_bifrost_src_DataStorage.tcc | 18 ++++++++++++++++++
 4 files changed, 27 insertions(+), 6 deletions(-)

diffs:
diff --git a/kallisto/DESCR b/kallisto/DESCR
index de9c8d8c3d..de04bdabe5 100644
--- a/kallisto/DESCR
+++ b/kallisto/DESCR
@@ -1,4 +1,5 @@
-Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
-data, or more generally of target sequences using high-throughput sequencing
-reads. It is based on the novel idea of pseudoalignment for rapidly determining
-the compatibility of reads with targets, without the need for alignment.
+Kallisto is a program for quantifying abundances of transcripts from
+RNA-Seq data, or more generally of target sequences using
+high-throughput sequencing reads. It is based on the novel idea of
+pseudoalignment for rapidly determining the compatibility of reads
+with targets, without the need for alignment.
diff --git a/kallisto/Makefile b/kallisto/Makefile
index 5b34565f9a..d1e3042be0 100644
--- a/kallisto/Makefile
+++ b/kallisto/Makefile
@@ -1,6 +1,7 @@
 # $NetBSD: Makefile,v 1.1 2018/12/21 19:00:56 bacon Exp $
 
 DISTNAME=	kallisto-0.51.1
+PKGREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=pachterlab/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
@@ -12,14 +13,13 @@ LICENSE=	2-clause-bsd
 
 USE_TOOLS+=	autoconf gmake pax
 USE_LANGUAGES=	c c++
-USE_CMAKE=	yes
 
 SUBST_CLASSES+=		test
 SUBST_STAGE.test=	pre-configure
 SUBST_FILES.test=	kallisto-test
 SUBST_SED.test=		-e 's|/usr/local/share/kallisto|${DATADIR}|g'
 
-CMAKE_CONFIGURE_ARGS+=		-DUSE_HDF5:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
+CMAKE_CONFIGURE_ARGS+=	-DUSE_HDF5:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 # Build fails on 8-core Mac M1
 MAKE_JOBS_SAFE=		no
 INSTALLATION_DIRS+=	${DATADIR}
@@ -34,6 +34,7 @@ post-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/kallisto-test ${DESTDIR}${PREFIX}/bin
 	cd ${WRKSRC} && pax -rw test ${DESTDIR}${DATADIR}
 
+.include "../../devel/cmake/build.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../archivers/libaec/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
diff --git a/kallisto/distinfo b/kallisto/distinfo
index 5f3dc2601f..8ea20b5aa0 100644
--- a/kallisto/distinfo
+++ b/kallisto/distinfo
@@ -7,6 +7,7 @@ SHA1 (patch-CMakeLists.txt) = 76746ef3999fca26d7cfe597172303ce7b023708
 SHA1 (patch-ext_bifrost_CMakeLists.txt) = 7b28282604691dc985c135f7048cc48fec1ae826
 SHA1 (patch-ext_bifrost_src_BitContainer.cpp) = 88a3b8b0d53bc4e96ec02f38f3f6e6bbd1e80dd7
 SHA1 (patch-ext_bifrost_src_ColorSet.cpp) = 55bb84a31ca97d21e6eefd44e2d3d6391f1e9304
+SHA1 (patch-ext_bifrost_src_DataStorage.tcc) = 832e68582e49af941778396b598bd45c766d948d
 SHA1 (patch-ext_bifrost_src_libpopcnt.h) = 3f31a47f40f341b1f6f72552b06990a81946e425
 SHA1 (patch-ext_bifrost_src_strict__fstream.hpp) = a4eab7784c3502fcc79ba0c87d31ac7275e5043c
 SHA1 (patch-src_Bootstrap.h) = 29a07a6fbaedf4387b70afb3b2caeb1a9b17f8e8
diff --git a/kallisto/patches/patch-ext_bifrost_src_DataStorage.tcc b/kallisto/patches/patch-ext_bifrost_src_DataStorage.tcc
new file mode 100644
index 0000000000..c9da1197a5
--- /dev/null
+++ b/kallisto/patches/patch-ext_bifrost_src_DataStorage.tcc
@@ -0,0 +1,18 @@
+$NetBSD$
+
+# Fix build with clang19
+
+--- ext/bifrost/src/DataStorage.tcc.orig	2025-05-27 13:48:42.121940805 +0000
++++ ext/bifrost/src/DataStorage.tcc
+@@ -78,7 +78,10 @@ DataStorage<U>::DataStorage(const DataSt
+ 
+         unitig_cs_link = new atomic<uint64_t>[sz_link];
+ 
+-        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
++	// Hayzam Sherif: o.sz_link -> o.unitig_cs_link
++	// Independently proposed by Lucas van Dijk:
++	// https://github.com/pmelsted/bifrost/pull/18/files
++        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
+     }
+ 
+     if ((o.data != nullptr) && (o.sz_cs != 0)){