From f2d7b3381bdfb39de7c07044ff47ee561feec8df Mon Sep 17 00:00:00 2001 From: natsukium Date: Thu, 8 Jun 2023 15:34:29 +0900 Subject: [PATCH 1/4] cmtk: 3.3.1 -> 3.3.2 --- pkgs/applications/science/biology/cmtk/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index 3eef64837255..44f413621d61 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -2,12 +2,12 @@ stdenv.mkDerivation rec { pname = "cmtk"; - version = "3.3.1"; + version = "3.3.2"; src = fetchurl { name = "cmtk-source.tar.gz"; - url = "https://www.nitrc.org/frs/download.php/8198/CMTK-${version}-Source.tar.gz//?i_agree=1&download_now=1"; - sha256 = "1nmsga9m7vcc4y4a6zl53ra3mwlgjwdgsq1j291awkn7zr1az6qs"; + url = "https://www.nitrc.org/frs/download.php/13188/CMTK-${version}-Source.tar.gz//?i_agree=1&download_now=1"; + hash = "sha256-iE164NCOSOypZLLZfZy9RTyrS+YnY9ECqfb4QhlsMS4="; }; nativeBuildInputs = [ cmake ]; From 6bf04fc9c9c099558f3355683a8aece21bbf15a3 Mon Sep 17 00:00:00 2001 From: natsukium Date: Fri, 7 Jul 2023 00:18:41 +0900 Subject: [PATCH 2/4] cmtk: fix darwin build --- pkgs/applications/science/biology/cmtk/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index 44f413621d61..7271d7389e04 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -13,12 +13,12 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; env.NIX_CFLAGS_COMPILE = toString [ - "-std=c++11" - (lib.optional stdenv.cc.isClang "-Wno-error=c++11-narrowing") + (lib.optionalString stdenv.cc.isGNU "-std=c++11") + (lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing") + (lib.optionalString (stdenv.isDarwin && stdenv.isAarch64) "-Dfinite=isfinite") ]; meta = with lib; { - broken = stdenv.isDarwin; description = "Computational Morphometry Toolkit "; longDescription = ''A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a From 7014b723d94b1814ccbd49c84e8bd6898acf5610 Mon Sep 17 00:00:00 2001 From: natsukium Date: Fri, 9 Jun 2023 15:28:27 +0900 Subject: [PATCH 3/4] cmtk: enable some compile options - use system zlib - enabled bzip2 - enabled fftw - enabled openmp for clang - still disabled Grand Central Dispatch for linux because of build failure - still disabled CUDA because of build failure - still disabled mxml because of build failure - still disabled lzma because of lack of lzmadec.h - still disabled dcmtk because of build failure --- .../science/biology/cmtk/default.nix | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index 7271d7389e04..b479d65b788d 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -1,4 +1,12 @@ -{ lib, stdenv, fetchurl, cmake }: +{ lib +, stdenv +, bzip2 +, cmake +, fetchurl +, fftw +, llvmPackages +, zlib +}: stdenv.mkDerivation rec { pname = "cmtk"; @@ -12,6 +20,14 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; + buildInputs = [ + bzip2 + fftw + zlib + ] ++ lib.optionals stdenv.cc.isClang [ + llvmPackages.openmp + ]; + env.NIX_CFLAGS_COMPILE = toString [ (lib.optionalString stdenv.cc.isGNU "-std=c++11") (lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing") From e7c8cbc2b17e21e451d9afdc468601d448d764f5 Mon Sep 17 00:00:00 2001 From: natsukium Date: Fri, 9 Jun 2023 17:19:17 +0900 Subject: [PATCH 4/4] cmtk: fix format - use finalAttrs instead of rec - fix license - remove trailing space from description --- pkgs/applications/science/biology/cmtk/default.nix | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index b479d65b788d..a131c6645499 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -8,13 +8,13 @@ , zlib }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "cmtk"; version = "3.3.2"; src = fetchurl { name = "cmtk-source.tar.gz"; - url = "https://www.nitrc.org/frs/download.php/13188/CMTK-${version}-Source.tar.gz//?i_agree=1&download_now=1"; + url = "https://www.nitrc.org/frs/download.php/13188/CMTK-${finalAttrs.version}-Source.tar.gz//?i_agree=1&download_now=1"; hash = "sha256-iE164NCOSOypZLLZfZy9RTyrS+YnY9ECqfb4QhlsMS4="; }; @@ -35,13 +35,13 @@ stdenv.mkDerivation rec { ]; meta = with lib; { - description = "Computational Morphometry Toolkit "; + description = "Computational Morphometry Toolkit"; longDescription = ''A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O''; maintainers = with maintainers; [ tbenst ]; platforms = platforms.all; - license = licenses.gpl3; + license = licenses.gpl3Plus; homepage = "https://www.nitrc.org/projects/cmtk/"; }; -} +})