CVS commit: pkgsrc/biology/kallisto

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Tue Aug 19 08:13:21 UTC 2025

Modified Files:
        pkgsrc/biology/kallisto: Makefile distinfo
        pkgsrc/biology/kallisto/patches: patch-ext_bifrost_CMakeLists.txt

Log Message:
kallisto: fix build with cmake 4


To generate a diff of this commit:
cvs rdiff -u -r1.10 -r1.11 pkgsrc/biology/kallisto/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/kallisto/distinfo
cvs rdiff -u -r1.3 -r1.4 \
    pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt

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

Modified files:

Index: pkgsrc/biology/kallisto/Makefile
diff -u pkgsrc/biology/kallisto/Makefile:1.10 pkgsrc/biology/kallisto/Makefile:1.11
--- pkgsrc/biology/kallisto/Makefile:1.10       Thu Mar  6 01:19:04 2025
+++ pkgsrc/biology/kallisto/Makefile    Tue Aug 19 08:13:20 2025
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.10 2025/03/06 01:19:04 bacon Exp $
+# $NetBSD: Makefile,v 1.11 2025/08/19 08:13:20 wiz Exp $
 
 DISTNAME=      kallisto-0.51.1
 CATEGORIES=    biology
@@ -19,7 +19,8 @@ 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
+CMAKE_CONFIGURE_ARGS+= -DCMAKE_POLICY_VERSION_MINIMUM=3.5
 # Build fails on 8-core Mac M1
 MAKE_JOBS_SAFE=                no
 INSTALLATION_DIRS+=    ${DATADIR}

Index: pkgsrc/biology/kallisto/distinfo
diff -u pkgsrc/biology/kallisto/distinfo:1.8 pkgsrc/biology/kallisto/distinfo:1.9
--- pkgsrc/biology/kallisto/distinfo:1.8        Fri Sep 20 00:03:15 2024
+++ pkgsrc/biology/kallisto/distinfo    Tue Aug 19 08:13:20 2025
@@ -1,10 +1,10 @@
-$NetBSD: distinfo,v 1.8 2024/09/20 00:03:15 bacon Exp $
+$NetBSD: distinfo,v 1.9 2025/08/19 08:13:20 wiz Exp $
 
 BLAKE2s (kallisto-0.51.1.tar.gz) = 30d30d14d54da30beb3f6b954546acec465a4029be99fb8b0faa353057dea994
 SHA512 (kallisto-0.51.1.tar.gz) = e5e7291e75c9d528bbb26691264a24480e1958e20eb56ce2f84192fe020b0b4c8485c9c143e19aedb0a988e6314acb312ea100cdb6c87c7cd895ef2908f7a149
 Size (kallisto-0.51.1.tar.gz) = 5954250 bytes
 SHA1 (patch-CMakeLists.txt) = 76746ef3999fca26d7cfe597172303ce7b023708
-SHA1 (patch-ext_bifrost_CMakeLists.txt) = 7b28282604691dc985c135f7048cc48fec1ae826
+SHA1 (patch-ext_bifrost_CMakeLists.txt) = 3a87264954d6d8757ddac6071c4bbdb684d5236f
 SHA1 (patch-ext_bifrost_src_BitContainer.cpp) = 88a3b8b0d53bc4e96ec02f38f3f6e6bbd1e80dd7
 SHA1 (patch-ext_bifrost_src_ColorSet.cpp) = 55bb84a31ca97d21e6eefd44e2d3d6391f1e9304
 SHA1 (patch-ext_bifrost_src_libpopcnt.h) = 3f31a47f40f341b1f6f72552b06990a81946e425

Index: pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt
diff -u pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.3 pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.4
--- pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt:1.3        Fri Sep 20 00:03:15 2024
+++ pkgsrc/biology/kallisto/patches/patch-ext_bifrost_CMakeLists.txt    Tue Aug 19 08:13:21 2025
@@ -1,9 +1,17 @@
-$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.3 2024/09/20 00:03:15 bacon Exp $
+$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.4 2025/08/19 08:13:21 wiz Exp $
+
+Fix build with cmake 4
 
 # Respect pkgsrc build flags
 
---- ext/bifrost/CMakeLists.txt.orig    2024-07-23 11:56:13.172038229 +0000
+--- ext/bifrost/CMakeLists.txt.orig    2024-09-17 05:40:08.000000000 +0000
 +++ ext/bifrost/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-cmake_minimum_required(VERSION 3.0.0)
++cmake_minimum_required(VERSION 3.5)
+ 
+ project(Bifrost)
+ 
 @@ -6,18 +6,12 @@ find_package(Threads REQUIRED)
  
  # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.