gentoo resync : 11.05.2021

12 files changed, 343 insertions, 54 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c910d9dc7469..9f51fb2222f9 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest
index b7356e9ae1b6..606b0c386d1e 100644
--- a/sci-biology/kallisto/Manifest
+++ b/sci-biology/kallisto/Manifest
@@ -1,4 +1,7 @@
-DIST kallisto-0.43.1.tar.gz 1067076 BLAKE2B 15a2fc65f0c9db431d9be6b2c8434b582ff7bf95fb659a9838d287feb3486744bca6201563d0f318be47c0f8532b805148a2eabfda633075d6b55bad1c3a406a SHA512 c7725a2d649cf96fcd24a20d542b409777cfd9fe97c09f0f459a5ec2981e0a4f5f0ea03d76d3ec3edf0e498c799fc7d074d442d5e35ddb4043d1f7634619dda8
-EBUILD kallisto-0.43.1.ebuild 573 BLAKE2B 895c8ccecb6b882cde7672208bf070f1b0de70ad15fadce89e0296f87a93d011a3de096d548bdb3e788e215767a7f6e0673c160fe82fb50fb4256653f9901a39 SHA512 bb8667422d4015ca7a3aad912385b5322b83c1122a99f79893f527c886cbc05049f2e37f7cc85d2c789994ebd477b9ff60019e4c91b7b95f65a51dd7343c4aff
-EBUILD kallisto-9999.ebuild 573 BLAKE2B 895c8ccecb6b882cde7672208bf070f1b0de70ad15fadce89e0296f87a93d011a3de096d548bdb3e788e215767a7f6e0673c160fe82fb50fb4256653f9901a39 SHA512 bb8667422d4015ca7a3aad912385b5322b83c1122a99f79893f527c886cbc05049f2e37f7cc85d2c789994ebd477b9ff60019e4c91b7b95f65a51dd7343c4aff
+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-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
 MISC metadata.xml 345 BLAKE2B de5a80ed6236a16fe08fb6a7eb815379edfa12af65db8c96a92b7494e8633661167152e1579fa886a13cc8060f0a68ac2646bc0a2321ce1fb39f9585bdc95511 SHA512 162700e5baed9b4696b90ecd014af596dca15a21bb27ffac4bc945c51701ec18e5cae963341670eb679873dfb54e22bfb9cb39299a5a00639e6afc6fd9f80412
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
new file mode 100644
index 000000000000..7566966c1c68
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-catch2.patch
@@ -0,0 +1,38 @@
+--- a/unit_tests/main.cpp
++++ b/unit_tests/main.cpp
+@@ -1,2 +1,2 @@
+ #define CATCH_CONFIG_MAIN
+-#include "catch.hpp"
++#include <catch2/catch.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 "common.h"
+ #include "KmerIndex.h"
+--- a/unit_tests/test_kmerhashtable.cpp
++++ b/unit_tests/test_kmerhashtable.cpp
+@@ -1,4 +1,4 @@
+-#include "catch.hpp"
++#include <catch2/catch.hpp>
+ 
+ #include <random>
+ #include <string>
+--- a/unit_tests/test_multinomial.cpp
++++ b/unit_tests/test_multinomial.cpp
+@@ -1,4 +1,4 @@
+-#include "catch.hpp"
++#include <catch2/catch.hpp>
+ 
+ #include <iostream>
+ #include <vector>
+--- a/unit_tests/test_weights.cpp
++++ b/unit_tests/test_weights.cpp
+@@ -1,4 +1,4 @@
+-#include "catch.hpp"
++#include <catch2/catch.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
new file mode 100644
index 000000000000..ba6114a9164f
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-cmake.patch
@@ -0,0 +1,149 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -11,9 +11,6 @@
+     add_compile_definitions("USE_HDF5=ON")
+ endif(USE_HDF5)
+ 
+-set(EXT_PROJECTS_DIR ${PROJECT_SOURCE_DIR}/ext)
+-set(CMAKE_CXX_FLAGS_PROFILE "-g")
+-
+ # Set Release type for builds where CMAKE_BUILD_TYPE is unset
+ # This is usually a good default as this implictly enables
+ #
+@@ -33,44 +30,12 @@
+     set(CMAKE_CXX_EXTENSIONS OFF)
+ endif()
+ 
+-#add_compile_options(-Wall -Wno-unused-function)
+-
+-if(LINK MATCHES static)
+-    message("static build")
+-ELSE(LINK MATCHES shared)
+-    message("shared build")
+-ENDIF(LINK MATCHES static)
+-
+-
+-include(ExternalProject)
+-ExternalProject_Add(htslib
+-    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
+-    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
+-    BUILD_IN_SOURCE 1
+-    CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure 
+-        --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl
+-    BUILD_COMMAND make lib-static
+-    INSTALL_COMMAND ""
+-)
+-
+-include_directories(${htslib_PREFIX}/src/htslib)
+-
+-
+-
+-# add_compile_options(-Wdeprecated-register)
+-
+ add_subdirectory(src)
+-include_directories(${EXT_PROJECTS_DIR})
+ 
+ option(BUILD_TESTING "Build unit tests." OFF)
+ include(CTest)
+ 
+ if (BUILD_TESTING)
+-    add_subdirectory(${EXT_PROJECTS_DIR}/catch)
+-
+-    # Includes Catch in the project:
+-    include_directories(${CATCH_INCLUDE_DIR} ${COMMON_INCLUDES})
+-
+     add_subdirectory(unit_tests)
+ endif(BUILD_TESTING)
+ 
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -3,30 +3,17 @@
+ 
+ list(REMOVE_ITEM sources main.cpp)
+ 
+-include_directories(../ext/htslib)
+-
+ add_library(kallisto_core ${sources} ${headers})
+ target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+ 
+ add_executable(kallisto main.cpp)
+ 
+-find_package( Threads REQUIRED )
+-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
+-
+-if(LINK MATCHES static)
+-    set(BUILD_SHARED_LIBS OFF)
+-    set(HDF5_USE_STATIC_LIBRARIES 1)
+-
+-    if (UNIX AND NOT APPLE)
+-        #set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libgcc -static-libstdc++")
+-        set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libstdc++")
+-        SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+-        set(CMAKE_EXE_LINKER_FLAGS  "-static -static-libgcc -static-libstdc++")
+-    endif(UNIX AND NOT APPLE)
+-
+-    SET_TARGET_PROPERTIES(kallisto kallisto_core PROPERTIES LINK_SEARCH_END_STATIC 1)
+-endif(LINK MATCHES static)
++find_package( PkgConfig REQUIRED )
++pkg_check_modules( HTSLIB REQUIRED htslib )
+ 
++find_package( Threads REQUIRED )
++target_include_directories(kallisto PRIVATE ${HTSLIB_CFLAGS})
++target_link_libraries(kallisto PRIVATE kallisto_core Threads::Threads ${HTSLIB_LDFLAGS})
+ 
+ if(USE_HDF5)
+     find_package( HDF5 REQUIRED )
+@@ -36,7 +23,7 @@
+ 
+ if ( ZLIB_FOUND )
+     include_directories( ${ZLIB_INCLUDE_DIRS} )
+-    target_link_libraries(kallisto kallisto_core ${ZLIB_LIBRARIES})
++    target_link_libraries(kallisto PRIVATE kallisto_core ${ZLIB_LIBRARIES})
+ else()
+     message(FATAL_ERROR "zlib not found. Required for to output files" )
+ endif( ZLIB_FOUND )
+@@ -44,22 +31,17 @@
+ if(USE_HDF5)
+     if(HDF5_FOUND)
+         include_directories( ${HDF5_INCLUDE_DIRS} )
+-        target_link_libraries( kallisto_core ${HDF5_LIBRARIES} )
+-        target_link_libraries( kallisto ${HDF5_LIBRARIES} )
++        target_link_libraries( kallisto_core PRIVATE ${HDF5_LIBRARIES} )
++        target_link_libraries( kallisto PRIVATE ${HDF5_LIBRARIES} )
+     else()
+         message(FATAL_ERROR "HDF5 not found. Required to output files")
+     endif()
+ endif(USE_HDF5)
+ 
+-if(LINK MATCHES static)
+-    if (UNIX AND NOT APPLE)
+-        target_link_libraries(kallisto librt.a)
+-    endif()
+-else()
+-    if (UNIX AND NOT APPLE)
+-        target_link_libraries(kallisto rt)
+-    endif()
+-endif(LINK MATCHES static)
+-
++target_compile_options( kallisto_core PRIVATE ${HTSLIB_CFLAGS} )
++target_link_libraries( kallisto_core PRIVATE ${HTSLIB_LDFLAGS} )
+ 
+-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
+\ No newline at end of file
++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
++if ( BUILD_SHARED_LIBS )
++    install(TARGETS kallisto_core DESTINATION "${CMAKE_INSTALL_LIBDIR}")
++endif()
+--- a/unit_tests/CMakeLists.txt
++++ b/unit_tests/CMakeLists.txt
+@@ -8,6 +8,10 @@
+ add_executable(tests ${sources})
+ add_test(unittest tests)
+ 
++find_package( Catch2 REQUIRED )
++include_directories( ${Catch2_INCLUDE_DIRS} )
++target_link_libraries( tests ${Catch2_LIBRARIES} )
++
+ find_package( ZLIB REQUIRED )
+ if ( ZLIB_FOUND )
+     include_directories( ${ZLIB_INCLUDE_DIRS} )
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch
new file mode 100644
index 000000000000..19594f067776
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-gcc11.patch
@@ -0,0 +1,21 @@
+From 1d63e9d731bada64f6038818e27f06da63007d73 Mon Sep 17 00:00:00 2001
+From: Nilesh Patra <npatra974@gmail.com>
+Date: Thu, 4 Mar 2021 23:38:30 +0530
+Subject: [PATCH] Fix GCC-11 Build Failure: include limits lib
+
+---
+ src/MinCollector.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/MinCollector.h b/src/MinCollector.h
+index a905f1f..c4460fb 100644
+--- a/src/MinCollector.h
++++ b/src/MinCollector.h
+@@ -7,6 +7,7 @@
+ #include <sstream>
+ #include <vector>
+ #include <unordered_map>
++#include <limits>
+ 
+ #include "KmerIndex.h"
+ #include "weights.h"
diff --git a/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch
new file mode 100644
index 000000000000..0e926136261c
--- /dev/null
+++ b/sci-biology/kallisto/files/kallisto-0.46.2-htslib.patch
@@ -0,0 +1,52 @@
+--- a/src/KmerIndex.cpp
++++ b/src/KmerIndex.cpp
+@@ -4,7 +4,7 @@
+ #include <ctype.h>
+ #include <zlib.h>
+ #include <unordered_set>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ 
+ #ifndef KSEQ_INIT_READY
+ #define KSEQ_INIT_READY
+--- a/src/ProcessReads.cpp
++++ b/src/ProcessReads.cpp
+@@ -1,6 +1,6 @@
+ /*
+ #include <zlib.h>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ #include <string>
+ #include <vector>
+ #include <unordered_map>
+@@ -20,7 +20,7 @@
+ #include <iomanip>
+ 
+ #include "ProcessReads.h"
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ #include "PseudoBam.h"
+ #include "Fusion.hpp"
+ #include "BUSData.h"
+--- a/src/ProcessReads.h
++++ b/src/ProcessReads.h
+@@ -2,7 +2,7 @@
+ #define KALLISTO_PROCESSREADS_H
+ 
+ #include <zlib.h>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ #include <string>
+ #include <vector>
+ #include <unordered_map>
+--- a/unit_tests/test_kmerhashtable.cpp
++++ b/unit_tests/test_kmerhashtable.cpp
+@@ -13,7 +13,7 @@
+ #include "KmerHashTable.h"
+ 
+ #include <zlib.h>
+-#include "kseq.h"
++#include <htslib/kseq.h>
+ 
+ #ifndef KSEQ_INIT_READY
+ #define KSEQ_INIT_READY
diff --git a/sci-biology/kallisto/kallisto-0.43.1.ebuild b/sci-biology/kallisto/kallisto-0.43.1.ebuild
deleted file mode 100644
index 0020e891a032..000000000000
--- a/sci-biology/kallisto/kallisto-0.43.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Near-optimal RNA-Seq quantification"
-HOMEPAGE="http://pachterlab.github.io/kallisto/"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
-else
-	SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-fi
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND="
-	sci-libs/hdf5:=
-	sys-libs/zlib:="
-DEPEND="${RDEPEND}"
diff --git a/sci-biology/kallisto/kallisto-0.46.2.ebuild b/sci-biology/kallisto/kallisto-0.46.2.ebuild
new file mode 100644
index 000000000000..293cf9f76ed0
--- /dev/null
+++ b/sci-biology/kallisto/kallisto-0.46.2.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="Near-optimal RNA-Seq quantification"
+HOMEPAGE="http://pachterlab.github.io/kallisto/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
+else
+	SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="hdf5 test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	sci-libs/htslib:=
+	sys-libs/zlib:=
+	hdf5? ( sci-libs/hdf5:= )"
+DEPEND="
+	${RDEPEND}
+	test? (
+		dev-cpp/catch:0
+		sci-libs/hdf5
+	)"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-cmake.patch
+	"${FILESDIR}"/${P}-htslib.patch
+	"${FILESDIR}"/${P}-catch2.patch
+	"${FILESDIR}"/${P}-gcc11.patch
+)
+
+src_prepare() {
+	cmake_src_prepare
+	# bundled catch2
+	rm -r ext || die
+	# bundled htslib structs
+	rm src/kseq.h || die
+
+	# the test suite is cheesy and relies on a
+	# specific builddir nesting structure.
+	sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \
+		-i unit_tests/test_kmerhashtable.cpp || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_HDF5=$(usex hdf5)
+		-DBUILD_TESTING=$(usex test)
+		# convenience library only
+		-DBUILD_SHARED_LIBS=OFF
+	)
+	cmake_src_configure
+}
diff --git a/sci-biology/kallisto/kallisto-9999.ebuild b/sci-biology/kallisto/kallisto-9999.ebuild
deleted file mode 100644
index 0020e891a032..000000000000
--- a/sci-biology/kallisto/kallisto-9999.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Near-optimal RNA-Seq quantification"
-HOMEPAGE="http://pachterlab.github.io/kallisto/"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
-else
-	SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-fi
-
-LICENSE="BSD"
-SLOT="0"
-
-RDEPEND="
-	sci-libs/hdf5:=
-	sys-libs/zlib:="
-DEPEND="${RDEPEND}"
diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest
index e7b206537f60..5517b87297b4 100644
--- a/sci-biology/treeviewx/Manifest
+++ b/sci-biology/treeviewx/Manifest
@@ -1,4 +1,5 @@
 AUX treeviewx-0.5.1-70_choose_tree.patch 347 BLAKE2B deb36ebad2fce531b353376d3e115bafad9a21ee7ac62ea7cc9571733e2565903f85e733fc27cef306bb82b038e2bd16c7a69a7666af2aa9c7a04ea04319f244 SHA512 8e83180f7619e61ab6a6cdce7a576820a8e12fc2c0caf73b68c3943a98c7e618fcf0d477276b976039b594d60388a80a24f0502ebbc45ec1be371946f5c0cf1e
+AUX treeviewx-0.5.1-AM_PROG_AR.patch 239 BLAKE2B efd6bd8e5c2b7e609e5e5184e3f31ecbd639a6c1ee4bdfa10a6c4f7d7f0c1b1cfb29efe95ef8ec886a6290858a009222b41739b0e8473ff5daa23b8930cddd31 SHA512 198c1158006ac01c1c3a1e0f35eb19c39fdf1e05ddf22908a640c1b74eb6779958fa086b7987e86582cee16ea086f64ae1083f2aeaf5b3abb6251e21870c1447
 AUX treeviewx-0.5.1-fix_loading_crash.patch 951 BLAKE2B 7fb391335a57114a9f8ee707ffe908839a064bbe6aeab05fe0b1af8928ccb0504d91ce9e25cc55a7762422f71978e28f1479adae11293249a8a67ce8536f8d05 SHA512 9c205520dce7851520b24532f88348906c4d5a7f0fe392348099ee9f7377b778792170620856d533a275251a024756482bbd4b83d1da8281b84c39cdf2b3a711
 AUX treeviewx-0.5.1-gcc4.3.patch 2601 BLAKE2B 740a3efb736389fa0de40b0f2344e2767450809547189ef6cf659b05b6d80954550b5d5688e03a904ce6f8ec45866dff174cda0dbdbee5b0baff8cef86992240 SHA512 4629ad00ca712163fccbdb029dbb42970d432b2bcaf6b6345a7bf3dca2331ab988742a6dfbc8874e2624988c699b4ba1fff8032dda53afcffbd8264df62b480b
 AUX treeviewx-0.5.1-svg.patch 1181 BLAKE2B b647b33738af0a933d0a946aa15d02f67b87175c4845813e9f01578dad6a3052902cc946b2f13dfe19451595364094094e388d8838c6c67b1448f8a32a832a65 SHA512 d71ee136f4f47792ce98826d8f7bca18320f404937abd90cdacd2685f62ed28f48601a105dd1cfb9717891a8930be339b6a663b11784f305d03af0cba24b4c4f
@@ -7,5 +8,5 @@ AUX treeviewx-0.5.1-wx30.patch 1722 BLAKE2B bc7d24b8b3953316ea4f8cb9eb26ab78fb7a
 AUX treeviewx-0.5.1-wxstring-maxlen.patch 1438 BLAKE2B a2dc6fe39c0312559628b61d86975a21db846e4c7cc3a0bb5739dd971417abd3ab9187ea56ef44d37c0394b28d4017981073eb4d890622d0d929f7a4d428950f SHA512 6e02ac59e8a28da8e94d5d6fdea71b3db9bc4501d9becf2d7aa6472d3f9f9b571fe68730390fd4cf6e1e422d618c21c40d86442d6b710e8395db107fc3445392
 AUX treeviewx-wxt.patch 1716 BLAKE2B f869d1d90dd23a7f0e242d9c1d0b0b97e0e053b5b2f00b283073f6e7f2d714cd2bf23656e65af1f3496bef0bf681ebb0618024f259b7f4d6dea777b048a438e4 SHA512 97d074e9501000099d0c5b3e3f56a796b1526499d4ccb44ef6f0b851bde1c27fc78bbc64f439ba5ecd3afa531b752c69148d7cd3b1e5a08a01566ad6155ce25c
 DIST tv-0.5.1.tar.gz 426745 BLAKE2B 080c4e09f441fd83da3406990bbe97f9e29fa531f47a65533ca887580f8a3ec561bb4766e66e2ef4764f68eee86fdabf48481cece56ddda90f9ffdc3c80b3a1a SHA512 45a7ac6dff5b22771e4428d6b1ee528c0039956a462658d28d4f588b6df32620d8f69b3bcf5ca23643e2bdd5361da00625fcb1495bcf4f74d44ee22022c63143
-EBUILD treeviewx-0.5.1-r3.ebuild 908 BLAKE2B 5d52ec68fa05f79848314599bb9b4a22378de9e26a5d958327f948780634a2de1a6155449968cc330f459525fb50ef28a5158e37bff9ae0e658174a2e92162a5 SHA512 92012299b8ca8dc97529c308e989258fd842e6c76bde1c267891afed198aa8c6ffd3b1f301b18c356613ecca47c32e61f60e2491d04a54d54f2eebfba874eb0d
+EBUILD treeviewx-0.5.1-r3.ebuild 945 BLAKE2B bdfd7f287e29287d8679657583ed738d2806e5dd175055a7c54058e14e4aba477509ae2a1a0677acdac3afad8030739f0511e1193059298cadb9e112ab75a36a SHA512 bb7bee425669dada45f106f0afdc5f7a6d2d17ea1fe56015c57a63402a6a0afcc777bffc06ac4cbc422dc03367cc4ef5633973260a845aaf78324f114a3182e1
 MISC metadata.xml 530 BLAKE2B e28ef45f05b4ade77b26155b743afe8e72989065c4dba57b7a645e738366afff1d99c827dc1ea1f5cdb192ae2ef790be6de9a6905eeebd58e792e5d4e02b0dcb SHA512 28c429150fb8df5db3205b352f077fe431f3e2ca530195468a340909a3b37882fae67e05452a7810ac34ffb8a02979625b48c28285a7d3abf31004238fce1463
diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-AM_PROG_AR.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-AM_PROG_AR.patch
new file mode 100644
index 000000000000..015c1ec65490
--- /dev/null
+++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-AM_PROG_AR.patch
@@ -0,0 +1,10 @@
+--- a/configure.in
++++ b/configure.in
+@@ -11,6 +11,7 @@
+ 
+ # We need ranlib to make the library, and we need to define make
+ AC_PROG_RANLIB
++AM_PROG_AR
+ AC_PROG_MAKE_SET
+ 
+ # Ensure that we set ENT (and set it to false). This flag affects
diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild
index 6ef3961e4df8..05e25ec750e9 100644
--- a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild
+++ b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild
@@ -27,6 +27,7 @@ PATCHES=(
 	"${FILESDIR}"/${P}-svg.patch
 	"${FILESDIR}"/${P}-treeview-xpm-not-xbm.patch
 	"${FILESDIR}"/${P}-wxstring-maxlen.patch
+	"${FILESDIR}"/${P}-AM_PROG_AR.patch
 )
 
 src_prepare() {