From 2b96a02432aeacb3a5f477be3477b95f8bd9d2ca Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Fri, 14 Jul 2023 11:10:49 -0500
Subject: [PATCH] biology/kallisto: Tag only for 64-bit architectures
Also patch out -march=native
Reported by: pkg-fallout
---
biology/kallisto/Makefile | 4 ++++
.../kallisto/files/patch-ext_bifrost_CMakeLists.txt | 11 +++++++++++
2 files changed, 15 insertions(+)
create mode 100644 biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 42715d9abc88..ea7cb1a53596 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,6 +1,7 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
DISTVERSION= 0.50.0
+PORTREVISION= 1
PORTEPOCH= 1
CATEGORIES= biology
@@ -11,6 +12,9 @@ WWW= https://pachterlab.github.io/kallisto/about.html
LICENSE= BSD2CLAUSE
LICENSE_FILE= ${WRKSRC}/license.txt
+# Requires a 64-bit processor
+ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64
+
LIB_DEPENDS= libhdf5.so:science/hdf5 \
libsz.so:science/libaec \
libhts.so:biology/htslib
diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
new file mode 100644
index 000000000000..c4c22a5e0666
--- /dev/null
+++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
@@ -0,0 +1,11 @@
+--- ext/bifrost/CMakeLists.txt.orig 2023-07-14 14:27:24 UTC
++++ ext/bifrost/CMakeLists.txt
+@@ -30,8 +30,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
+ message("Disabling native architecture compilation (including AVX2)")
+ else(COMPILATION_ARCH MATCHES "OFF")
+ message("Compilation architecture: ${COMPILATION_ARCH}")
+- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=${COMPILATION_ARCH}")
+- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${COMPILATION_ARCH}")
+ endif(COMPILATION_ARCH MATCHES "OFF")
+
+ if(ENABLE_AVX2 MATCHES "OFF")
--
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