gentoo auto-resync : 07:04:2024 - 12:30:41

5 files changed, 17 insertions, 13 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 0038f5895b89..c743269e5a52 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest
index fa15e14e7cdd..2916a51b0f3c 100644
--- a/sci-biology/kallisto/Manifest
+++ b/sci-biology/kallisto/Manifest
@@ -1,7 +1,7 @@
-AUX kallisto-0.46.2-catch2.patch 854 BLAKE2B b31810e9defde5cad8dc90dca93d708b2518c42ccf3ae4e93fe303ee98c7f4ab25043614416733057084b2433fc075f8281b6a852e4cdf720069cdb682a1a14c SHA512 2f0c02dab09d957b5f125169d1fa45445c3d9a43c65f59ad62ecdbac310793f3b98e1e0e814160f657f4b1e09bb1eea48002d9227764f687d376c56bb3aa4666
-AUX kallisto-0.46.2-cmake.patch 4643 BLAKE2B 1f078335d8fb25116db7dfd8527b93950d996975987fa0779dcaf951c2f86390e8c82d0f0a684414fd0aedbce22203276ac4a96369ab79b0e283be25154a7add SHA512 7db08dfcdc5bb2fe8ba1cc43f0bf6874589df16ff01b162cdb6c57892ce99ded4e60d8726d987aa42c6d1e8d1534f26547f73474aaa1c72be05aad2019d23ebb
+AUX kallisto-0.46.2-catch2.patch 874 BLAKE2B afc0550e1999bb37d39799f2beb646e4e23b729b6b444919663837de5c92e9abadd574988ecc9edbc5fddfebbb36e4a404070df8c6269ee9e8b83207eccdb0f4 SHA512 24b347761df6170efdc555754779cd7ac07eea96179637b323e90f2500679fe231d85a13d10f0af9dde68e02ffbbd9dd5286f0dfe4237fb8f07b49ddaa954869
+AUX kallisto-0.46.2-cmake.patch 4646 BLAKE2B 43795b1a248448043ed2bfa5046cbeb926236e9c5e89b772257577eaa3044f402d5db4bbacf224d0a18005df5b74580a29b6514552cfb353caf61c9f782fadde SHA512 269a0c197930d53e1b46d0362bc4018bf1eccc98c2b9e90a342e8e000a7741cc9be43d0843ebe4702d9b90113a3654e457197ceaff4001ac3b3704be4d683746
 AUX kallisto-0.46.2-gcc11.patch 556 BLAKE2B 96750a155c248714b254842033a58db7f2cac94ad18e6c289e9d201b108d4f497a55f7f9e0323a42cbc0aad7ae56fa9c5cc82ad7bcd3d159dae6a93ac544548d SHA512 0e32eb4d17cf7708def2f67d7b152dbab3c7977f54e7f2537052508633272d62fba9b2acbfbfba8fc77873208d410b16f4393f12c0c262436e2f6775c8aa3316
 AUX kallisto-0.46.2-htslib.patch 1082 BLAKE2B d00487073fb0e9fdd6cfe07d14dadc1f23c043a793381969073ef74ea6798d48dad5a3a5d3411271f6fcb02a84c5bdbc4d35d31a916cbea2341137384e3ec16e SHA512 61ddfc3099c70e1bd448c43c1cc490a5d00effe5ccdcc0904c7c3d275282e2c1bb5ed8ed41cadf03c28b36b208db73cfa61ec7883116575e9b64941e1b0ca818
 DIST kallisto-0.46.2.tar.gz 2693869 BLAKE2B 73d725e74133d64b9f7910f69a5fff85eac05b93ad6891807a6fd4e16a1fa16a55306058db3fcb4e0fbfeb0719d3a9d3c8da7d2b76b64dde5a2fea51b0254b99 SHA512 6aca29afa0abe1c6896d27745fd2436c9b9aaf298d70276baf877dbf0aaaba94df54b9a42829c8f8f7c02e7262ecd1837b8a021625c3066a10c0cc0551179093
-EBUILD kallisto-0.46.2.ebuild 1385 BLAKE2B 0100f200cd014b54aa3b3efe45992f2c1c0a71dec5a3a349e47750b4d9853ebff4a70d6db017c761e64ccb7f73bec5222fbe8f2caea28d1b473e24d5d41fb0c4 SHA512 079559274c42faad8b090dd0d4d71da226a4e161051f9a10af949ea3b2f3aa3631222e31934bc225d7f15536f99ba31ec881296fc5f15324f14a526e5ef8788a
+EBUILD kallisto-0.46.2-r1.ebuild 1573 BLAKE2B 85cc1c4b9aee4e1600376bd1cdff66d15ed2d9fde8ddbacff48366b7543db192b50a4a17bddd21dfb5d60b0bc07f8896bb774f4f67a823147bbc4aa4919d6c9e SHA512 13fb422d24688c034e257c092da2538bbd9882c73732011c4604e95d7ffe1e2f77eabf514f4382764a0cdeb30f8788120c525e297e00358567bec15dbabbb86a
 MISC metadata.xml 346 BLAKE2B bcf0798fe760534c24a61acbc8f7775c1ab8d22abb7da232f1829d609006a435f519f8e4006ee3c0a79677efc39d9747786ebf393a0373e6d53aabe218da9ac9 SHA512 fcc275ff592a083f82eadbbbb2d71085286fba3307d9316ddc87f18994ae652b468b5a4314b763189a0f789d262da31769d21730f80340ace2095a008276993d
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
index 7566966c1c68..3ff6a0c33be0 100644
--- a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
@@ -3,12 +3,12 @@
 @@ -1,2 +1,2 @@
  #define CATCH_CONFIG_MAIN
 -#include "catch.hpp"
-+#include <catch2/catch.hpp>
++#include <catch2/catch_all.hpp>
 --- a/unit_tests/test_index.cpp
 +++ b/unit_tests/test_index.cpp
 @@ -1,4 +1,4 @@
 -#include "catch.hpp"
-+#include <catch2/catch.hpp>
++#include <catch2/catch_all.hpp>
  
  #include "common.h"
  #include "KmerIndex.h"
@@ -16,7 +16,7 @@
 +++ b/unit_tests/test_kmerhashtable.cpp
 @@ -1,4 +1,4 @@
 -#include "catch.hpp"
-+#include <catch2/catch.hpp>
++#include <catch2/catch_all.hpp>
  
  #include <random>
  #include <string>
@@ -24,7 +24,7 @@
 +++ b/unit_tests/test_multinomial.cpp
 @@ -1,4 +1,4 @@
 -#include "catch.hpp"
-+#include <catch2/catch.hpp>
++#include <catch2/catch_all.hpp>
  
  #include <iostream>
  #include <vector>
@@ -32,7 +32,7 @@
 +++ b/unit_tests/test_weights.cpp
 @@ -1,4 +1,4 @@
 -#include "catch.hpp"
-+#include <catch2/catch.hpp>
++#include <catch2/catch_all.hpp>
  
  #include <vector>
  
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
index ba6114a9164f..6516f162e906 100644
--- a/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
@@ -142,7 +142,7 @@
  
 +find_package( Catch2 REQUIRED )
 +include_directories( ${Catch2_INCLUDE_DIRS} )
-+target_link_libraries( tests ${Catch2_LIBRARIES} )
++target_link_libraries( tests Catch2::Catch2WithMain )
 +
  find_package( ZLIB REQUIRED )
  if ( ZLIB_FOUND )
diff --git a/sci-biology/kallisto/kallisto-0.46.2.ebuild b/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild
index 293cf9f76ed0..68640687cf9d 100644
--- a/sci-biology/kallisto/kallisto-0.46.2.ebuild
+++ b/sci-biology/kallisto/kallisto-0.46.2-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-inherit cmake
+inherit cmake flag-o-matic
 
 DESCRIPTION="Near-optimal RNA-Seq quantification"
 HOMEPAGE="http://pachterlab.github.io/kallisto/"
@@ -28,7 +28,7 @@ RDEPEND="
 DEPEND="
 	${RDEPEND}
 	test? (
-		dev-cpp/catch:0
+		>=dev-cpp/catch-3:0
 		sci-libs/hdf5
 	)"
 BDEPEND="virtual/pkgconfig"
@@ -51,6 +51,10 @@ src_prepare() {
 	# specific builddir nesting structure.
 	sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \
 		-i unit_tests/test_kmerhashtable.cpp || die
+
+	# This randomly hardcodes a particular std, which unfortunately is too old for catch2.
+	sed -i '/CMAKE_CXX_STANDARD/d' CMakeLists.txt || die
+	append-cxxflags -std=c++14
 }
 
 src_configure() {