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CVS commit: pkgsrc/biology/canu
Module Name: pkgsrc
Committed By: bacon
Date: Sat May 20 14:42:11 UTC 2023
Modified Files:
pkgsrc/biology/canu: Makefile PLIST distinfo
pkgsrc/biology/canu/patches: patch-Makefile
patch-pipelines_canu_Defaults.pm patch-pipelines_canu_Execution.pm
patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
patch-utility_src_utility_files.H
patch-utility_src_utility_logging.H
patch-utility_src_utility_system.H
patch-utility_src_utility_types.H
Added Files:
pkgsrc/biology/canu/files: cpuid_arm.c cpuid_ppc.c
Log Message:
biology/canu: Fix build on Darwin aarch64
Replace SIMDE with upstream source hacks from FreeBSD port
Should also work on powerpc, but untested
No changes to existing binaries
To generate a diff of this commit:
cvs rdiff -u -r1.20 -r1.21 pkgsrc/biology/canu/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/canu/PLIST
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/canu/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/canu/files/cpuid_arm.c \
pkgsrc/biology/canu/files/cpuid_ppc.c
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/canu/patches/patch-Makefile \
pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm \
pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm
cvs rdiff -u -r1.2 -r1.3 \
pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp \
pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H \
pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H \
pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H \
pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/biology/canu/Makefile
diff -u pkgsrc/biology/canu/Makefile:1.20 pkgsrc/biology/canu/Makefile:1.21
--- pkgsrc/biology/canu/Makefile:1.20 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/Makefile Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.20 2023/05/20 11:27:27 bacon Exp $
+# $NetBSD: Makefile,v 1.21 2023/05/20 14:42:11 bacon Exp $
DISTNAME= canu-2.2
CATEGORIES= biology java
@@ -31,7 +31,7 @@ REPLACE_PERL+= fastq-utilities/*.pl
REPLACE_PERL+= *.pl
# May work on other 64-bit processors, but untested
-ONLY_FOR_PLATFORM= *-*-x86_64 *-*-aarch64
+ONLY_FOR_PLATFORM= *-*-x86_64 *-*-aarch64 *-*-powerpc64
USE_LANGUAGES= c c++
USE_JAVA= run
@@ -46,8 +46,15 @@ SITE_PERL_REL= lib/perl5/site_perl
JAVAJARDIR= share/java/classes
INSTALLATION_DIRS= bin lib/perl5 ${JAVAJARDIR}
+.include "../../mk/bsd.prefs.mk"
+
post-extract:
${CHMOD} -R g-w ${WRKDIR}
+.if ${MACHINE_ARCH} == "aarch64"
+ ${CP} ${FILESDIR}/cpuid_arm.c ${WRKSRC}/utility/src/parasail/cpuid.c
+.elif ${MACHINE_ARCH} == "powerpc64"
+ ${CP} ${FILESDIR}/cpuid_ppc.c ${WRKSRC}/utility/src/parasail/cpuid.c
+.endif
# Upstream does not want to use lib/perl5/site_perl
post-build:
@@ -59,8 +66,6 @@ do-install:
cd ${TMP_INST}/lib/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5
cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share
-.include "../../mk/bsd.prefs.mk"
-
# Xcode supports -Xpreprocessor -fopenmp, but does not supply OpenMP libs
# parallel/openmp installs an entire llvm
# Maybe a libomp package would suffice?
@@ -69,6 +74,5 @@ do-install:
.endif
.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../devel/simde/buildlink3.mk"
.include "../../lang/perl5/module.mk"
.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/canu/PLIST
diff -u pkgsrc/biology/canu/PLIST:1.3 pkgsrc/biology/canu/PLIST:1.4
--- pkgsrc/biology/canu/PLIST:1.3 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/PLIST Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2023/05/20 11:27:27 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2023/05/20 14:42:11 bacon Exp $
bin/alignGFA
bin/bogart
bin/canu
Index: pkgsrc/biology/canu/distinfo
diff -u pkgsrc/biology/canu/distinfo:1.6 pkgsrc/biology/canu/distinfo:1.7
--- pkgsrc/biology/canu/distinfo:1.6 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/distinfo Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: distinfo,v 1.6 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: distinfo,v 1.7 2023/05/20 14:42:11 bacon Exp $
BLAKE2s (canu-2.2.tar.xz) = 5b585a2e0a31c2181817798b5f267dd4cf43c3ffeba4b0a04ffc8021a4603aed
SHA512 (canu-2.2.tar.xz) = af08874a319dd5fd6bbe666c8a5d0a43b7c0caaaca3a3cbf4d3fe022d6d6b8c14cd967c2e26f4fbf571129be240dcb65e92fe61fad1e51d554f15254d0b6ce8f
@@ -7,8 +7,6 @@ SHA1 (patch-Makefile) = 54a3a216948fea81
SHA1 (patch-pipelines_canu_Defaults.pm) = 5ecea8ebac667499916b0243f34dc25838992444
SHA1 (patch-pipelines_canu_Execution.pm) = 75c019a93f5b6a4491191b4f32931ac0b8435421
SHA1 (patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp) = fd219645141ebe9d6f23153a2a2b0f56abc103af
-SHA1 (patch-utility_src_parasail_internal__sse.h) = 3eca097b64273ada2df6f9be895823980ea79902
-SHA1 (patch-utility_src_utility_align-ssw.H) = 146e1959207dfe1deaae7f8f9809ed72be116841
SHA1 (patch-utility_src_utility_files.H) = bc28dfd6957a2e2928b5df6a0e1d08c8ba5b2c27
SHA1 (patch-utility_src_utility_logging.H) = 13e9ced966710cef4a2d38fd2b752f8a726ba07b
SHA1 (patch-utility_src_utility_system.H) = e0bab7ed20431948845fac907584215c0b891406
Index: pkgsrc/biology/canu/patches/patch-Makefile
diff -u pkgsrc/biology/canu/patches/patch-Makefile:1.3 pkgsrc/biology/canu/patches/patch-Makefile:1.4
--- pkgsrc/biology/canu/patches/patch-Makefile:1.3 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-Makefile Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.3 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-Makefile,v 1.4 2023/05/20 14:42:11 bacon Exp $
# Portability
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm
diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.3 pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.4
--- pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.3 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.4 2023/05/20 14:42:11 bacon Exp $
# Better task limit control under slurm
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm
diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.3 pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.4
--- pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.3 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-pipelines_canu_Execution.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-pipelines_canu_Execution.pm,v 1.4 2023/05/20 14:42:11 bacon Exp $
# Better task limit control under slurm
Index: pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
diff -u pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.2 pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.3
--- pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.2 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.2 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.3 2023/05/20 14:42:11 bacon Exp $
# Portability
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.3
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.2 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_files.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-utility_src_utility_files.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
# Portability
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.3
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.2 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_logging.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-utility_src_utility_logging.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
# Portability
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.3
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.2 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_system.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-utility_src_utility_system.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
# Portability
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.3
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.2 Sat May 20 11:27:27 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H Sat May 20 14:42:11 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_types.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
+$NetBSD: patch-utility_src_utility_types.H,v 1.3 2023/05/20 14:42:11 bacon Exp $
# Portability
Added files:
Index: pkgsrc/biology/canu/files/cpuid_arm.c
diff -u /dev/null pkgsrc/biology/canu/files/cpuid_arm.c:1.1
--- /dev/null Sat May 20 14:42:12 2023
+++ pkgsrc/biology/canu/files/cpuid_arm.c Sat May 20 14:42:11 2023
@@ -0,0 +1,57 @@
+/**
+ * @file
+ *
+ * @author jeffrey.daily%gmail.com@localhost
+ *
+ * Copyright (c) 2015 Battelle Memorial Institute.
+ *
+ * For non-intel platforms, stub out the intel feature tests.
+ */
+#include "config.h"
+
+#include "parasail/cpuid.h"
+
+int parasail_can_use_avx512vbmi()
+{
+ return 0;
+}
+
+int parasail_can_use_avx512bw()
+{
+ return 0;
+}
+
+int parasail_can_use_avx512f()
+{
+ return 0;
+}
+
+int parasail_can_use_avx2()
+{
+ return 0;
+}
+
+int parasail_can_use_sse41()
+{
+ return 0;
+}
+
+int parasail_can_use_sse2()
+{
+ return 0;
+}
+
+int parasail_can_use_altivec()
+{
+ return 0;
+}
+
+int parasail_can_use_neon()
+{
+#if HAVE_NEON
+ return 1;
+#else
+ return 0;
+#endif
+}
+
Index: pkgsrc/biology/canu/files/cpuid_ppc.c
diff -u /dev/null pkgsrc/biology/canu/files/cpuid_ppc.c:1.1
--- /dev/null Sat May 20 14:42:12 2023
+++ pkgsrc/biology/canu/files/cpuid_ppc.c Sat May 20 14:42:11 2023
@@ -0,0 +1,57 @@
+/**
+ * @file
+ *
+ * @author jeffrey.daily%gmail.com@localhost
+ *
+ * Copyright (c) 2015 Battelle Memorial Institute.
+ *
+ * For non-intel platforms, stub out the intel feature tests.
+ */
+#include "config.h"
+
+#include "parasail/cpuid.h"
+
+int parasail_can_use_avx512vbmi()
+{
+ return 0;
+}
+
+int parasail_can_use_avx512bw()
+{
+ return 0;
+}
+
+int parasail_can_use_avx512f()
+{
+ return 0;
+}
+
+int parasail_can_use_avx2()
+{
+ return 0;
+}
+
+int parasail_can_use_sse41()
+{
+ return 0;
+}
+
+int parasail_can_use_sse2()
+{
+ return 0;
+}
+
+int parasail_can_use_altivec()
+{
+#if HAVE_ALTIVEC
+ return 1;
+#else
+ return 0;
+#endif
+}
+
+int parasail_can_use_neon()
+{
+ return 0;
+}
+
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