From cda3541bff2b138dceaf76d53e453cc67b423e56 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Tue, 26 Jul 2022 15:10:26 -0400
Subject: [PATCH 1/2] libminc: unstable-2020-07-17 -> 2.4.05

- hdf5_1_10 -> hdf5
- enable previously erroring test
---
 pkgs/development/libraries/libminc/default.nix | 12 ++++++------
 pkgs/top-level/all-packages.nix                |  4 +---
 2 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/libraries/libminc/default.nix b/pkgs/development/libraries/libminc/default.nix
index f1f6dc1b374f..00db5fc83377 100644
--- a/pkgs/development/libraries/libminc/default.nix
+++ b/pkgs/development/libraries/libminc/default.nix
@@ -2,15 +2,15 @@
 
 stdenv.mkDerivation rec {
   pname   = "libminc";
-  version = "unstable-2020-07-17";
+  version = "2.4.05";
 
   owner = "BIC-MNI";
 
   src = fetchFromGitHub {
     inherit owner;
     repo   = pname;
-    rev    = "ffb5fb234a852ea7e8da8bb2b3b49f67acbe56ca";
-    sha256 = "0yr4ksghpvxh9zg0a4p7hvln3qirsi08plvjp5kxx2qiyj96zsdm";
+    rev    = "aa08255f0856e70fb001c5f9ee1f4e5a8c12d47d";  # new release, but no git tag
+    sha256 = "XMTO6/HkyrrQ0s5DzJLCmmWheye2DGMnpDbcGdP6J+A=";
   };
 
   postPatch = ''
@@ -24,14 +24,14 @@ stdenv.mkDerivation rec {
   cmakeFlags = [
     "-DLIBMINC_MINC1_SUPPORT=ON"
     "-DLIBMINC_BUILD_SHARED_LIBS=ON"
+    "-DLIBMINC_USE_NIFTI=ON"
     "-DLIBMINC_USE_SYSTEM_NIFTI=ON"
   ];
 
   doCheck = !stdenv.isDarwin;
-  checkPhase = ''
-    ctest -j1 -E 'ezminc_rw_test' --output-on-failure
     # -j1: see https://github.com/BIC-MNI/libminc/issues/110
-    # ezminc_rw_test: can't find libminc_io.so.5.2.0
+  checkPhase = ''
+    ctest -j1 --output-on-failure
   '';
 
   meta = with lib; {
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index e449c34634bd..716a613989ee 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -19440,9 +19440,7 @@ with pkgs;
 
   libmilter = callPackage ../development/libraries/libmilter { };
 
-  libminc = callPackage ../development/libraries/libminc {
-    hdf5 = hdf5_1_10;
-  };
+  libminc = callPackage ../development/libraries/libminc { };
 
   libmkv = callPackage ../development/libraries/libmkv { };
 

From 125da198662adacbeb31d247b96eabdcb2dc3462 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Tue, 26 Jul 2022 15:47:22 -0400
Subject: [PATCH 2/2] mni_autoreg: unstable-2017-02-22 -> unstable-2022-05-20

---
 .../science/biology/mni_autoreg/default.nix    | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix
index d7882bd4854e..29ab02ee3139 100644
--- a/pkgs/applications/science/biology/mni_autoreg/default.nix
+++ b/pkgs/applications/science/biology/mni_autoreg/default.nix
@@ -1,26 +1,16 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, perlPackages, libminc }:
+{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc }:
 
 stdenv.mkDerivation rec {
   pname = "mni_autoreg";
-  version = "unstable-2017-09-22";
+  version = "unstable-2022-05-20";
 
   src = fetchFromGitHub {
     owner = "BIC-MNI";
     repo = pname;
-    rev = "ab99e29987dc029737785baebf24896ec37a2d76";
-    sha256 = "0axl069nv57vmb2wvqq7s9v3bfxwspzmk37bxm4973ai1irgppjq";
+    rev = "be7bd25bf7776974e0f2c1d90b6e7f8ccc0c8874";
+    sha256 = "sGMZbCrdV6yAOgGiqvBFOUr6pGlTCqwy8yNrPxMoKco=";
   };
 
-  patches = [
-    # Pull upstream workaround for -fno-common toolchains:
-    #  https://github.com/BIC-MNI/mni_autoreg/pull/28
-    (fetchpatch {
-      name = "fno-common.patch";
-      url = "https://github.com/BIC-MNI/mni_autoreg/commit/06adfacbd84369ea3bcc4376596ac1c0f2e49af9.patch";
-      sha256 = "004sdrbx9kcj1qqwjly6p03svakl0x2sbv83salyg63fv67jynx8";
-    })
-  ];
-
   nativeBuildInputs = [ cmake makeWrapper ];
   buildInputs = [ libminc ];
   propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ];