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Merge pull request #93675 from bcdarwin/update-libminc

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libminc: 2.4.03 -> unstable-2020-07-17
This commit is contained in:
Linus Heckemann 2020-10-07 08:08:10 +02:00 committed by GitHub
parent c7b3d98659 95439a7e7d
commit a25bd6604f
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GPG key ID: 4AEE18F83AFDEB23
14 changed files with 41 additions and 138 deletions
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4
pkgs/applications/science/biology/EZminc/default.nix
View file

@ -2,7 +2,7 @@
stdenv.mkDerivation rec {
pname = "EZminc";
name = "${pname}-unstable-2019-03-12";
version = "unstable-2019-03-12";
src = fetchFromGitHub {
owner = "BIC-MNI";
@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake pkgconfig ];
buildInputs = [ itk4 libminc bicpl fftwFloat gsl ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DEZMINC_BUILD_TOOLS=TRUE"
"-DEZMINC_BUILD_MRFSEG=TRUE"
"-DEZMINC_BUILD_DD=TRUE" ];

10
pkgs/applications/science/biology/N3/default.nix
View file

@ -4,20 +4,20 @@
stdenv.mkDerivation rec {
pname = "N3";
name = "${pname}-2017-09-18";
version = "unstable-2018-08-09";
src = fetchFromGitHub {
owner = "BIC-MNI";
repo = pname;
rev = "2fdd939f0f2b24a4039bc6a8ade4a190a1d8e75d";
sha256 = "13z21c4r09hna3q1csvcn4i7ws5ixbdaja6ch421xv6nydjh2w5g";
rev = "010fc2ac58ce1d67b8e6a863fac0809d3203cb9b";
sha256 = "06hci7gzhy8p34ggvx7gah2k9yxpwhgmq1cgw8pcd1r82g4rg6kd";
};
nativeBuildInputs = [ cmake makeWrapper ];
buildInputs = [ libminc EBTKS ];
propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ];
postFixup = ''
for p in $out/bin/*; do
@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
'';
meta = with stdenv.lib; {
homepage = "https://github.com/BIC-MNI/${pname}";
homepage = "https://github.com/BIC-MNI/N3";
description = "MRI non-uniformity correction for MINC files";
maintainers = with maintainers; [ bcdarwin ];
platforms = platforms.unix;

7
pkgs/applications/science/biology/conglomerate/default.nix
View file

@ -3,7 +3,7 @@
stdenv.mkDerivation rec {
pname = "conglomerate";
name = "${pname}-2017-09-10";
version = "unstable-2017-09-10";
src = fetchFromGitHub {
owner = "BIC-MNI";
@ -16,7 +16,10 @@ stdenv.mkDerivation rec {
buildInputs = [ libminc zlib bicpl ];
propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]);
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBICPL_DIR=${bicpl}/lib/" ];
cmakeFlags = [
"-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DBICPL_DIR=${bicpl}/lib"
];
postFixup = ''
for p in $out/bin/*; do

2
pkgs/applications/science/biology/inormalize/default.nix
View file

@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
buildInputs = [ libminc EBTKS ];
propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ];
postFixup = ''
for p in $out/bin/*; do

16
pkgs/applications/science/biology/minc-tools/default.nix
View file

@ -3,28 +3,20 @@
stdenv.mkDerivation rec {
pname = "minc-tools";
version = "unstable-2019-12-04";
version = "unstable-2020-07-25";
src = fetchFromGitHub {
owner = "BIC-MNI";
repo = pname;
rev = "d4dddfdb4e4fa0cea389b8fdce51cfc076565d94";
sha256 = "1wwdss59qq4hz1jp35qylfswzzv0d37if23al0srnxkkgc5f8zng";
rev = "fb0a68a07d281e4e099c5d54df29925240de14c1";
sha256 = "0zcv2sdj3k6k0xjqdq8j5bxq8smm48dzai90vwsmz8znmbbm6kvw";
};
patches = [ ./fix-netcdf-header.patch ];
# add missing CMake module to build NIFTI support
# (the maintainers normally build libminc and minc-tools in a meta-project)
postPatch = ''
cp ${libminc.src}/cmake-modules/FindNIFTI.cmake cmake-modules
'';
nativeBuildInputs = [ cmake flex bison makeWrapper ];
buildInputs = [ libminc libjpeg nifticlib zlib ];
propagatedBuildInputs = [ perl TextFormat ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DZNZ_INCLUDE_DIR=${nifticlib}/include/nifti"
"-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti" ];

12
pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch
View file

@ -1,12 +0,0 @@
diff --git a/progs/mincdump/mincdump.h b/progs/mincdump/mincdump.h
index 14c95cd..117ab26 100644
--- a/progs/mincdump/mincdump.h
+++ b/progs/mincdump/mincdump.h
@@ -3,6 +3,7 @@
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header: /private-cvsroot/minc/progs/mincdump/mincdump.h,v 1.1 2004-04-27 15:35:15 bert Exp $
*********************************************************************/
+#include <netcdf_meta.h>
/* error checking macro */

4
pkgs/applications/science/biology/mni_autoreg/default.nix
View file

@ -2,7 +2,7 @@
stdenv.mkDerivation rec {
pname = "mni_autoreg";
name = "${pname}-2017-09-22";
version = "unstable-2017-09-22";
src = fetchFromGitHub {
owner = "BIC-MNI";
@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
buildInputs = [ libminc ];
propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
# testing broken: './minc_wrapper: Permission denied' from Testing/ellipse0.mnc
postFixup = ''

20
pkgs/development/libraries/libminc/default.nix
View file

@ -2,15 +2,15 @@
stdenv.mkDerivation rec {
pname = "libminc";
version = "2.4.03";
version = "unstable-2020-07-17";
owner = "BIC-MNI";
src = fetchFromGitHub {
inherit owner;
repo = pname;
rev = "release-${version}";
sha256 = "0kpmqs9df836ywsqj749qbsfavf5bnldblxrmnmxqq9pywc8yfrm";
rev = "ffb5fb234a852ea7e8da8bb2b3b49f67acbe56ca";
sha256 = "0yr4ksghpvxh9zg0a4p7hvln3qirsi08plvjp5kxx2qiyj96zsdm";
};
postPatch = ''
@ -18,7 +18,8 @@ stdenv.mkDerivation rec {
'';
nativeBuildInputs = [ cmake ];
buildInputs = [ zlib netcdf nifticlib hdf5 ];
buildInputs = [ zlib nifticlib ];
propagatedBuildInputs = [ netcdf hdf5 ];
cmakeFlags = [
"-DLIBMINC_MINC1_SUPPORT=ON"
@ -29,17 +30,16 @@ stdenv.mkDerivation rec {
doCheck = !stdenv.isDarwin;
checkPhase = ''
export LD_LIBRARY_PATH="$(pwd)" # see #22060
ctest -E 'ezminc_rw_test|minc_conversion' --output-on-failure
# ezminc_rw_test can't find libminc_io.so.5.2.0; minc_conversion hits netcdf compilation issue
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
'';
enableParallelBuilding = true;
meta = with stdenv.lib; {
homepage = "https://github.com/${owner}/${pname}";
homepage = "https://github.com/BIC-MNI/libminc";
description = "Medical imaging library based on HDF5";
maintainers = with maintainers; [ bcdarwin ];
platforms = platforms.unix;
license = licenses.free;
license = licenses.free;
};
}

2
pkgs/development/libraries/science/biology/EBTKS/default.nix
View file

@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake ];
buildInputs = [ libminc ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
meta = with stdenv.lib; {
homepage = "https://github.com/BIC-MNI/${pname}";

9
pkgs/development/libraries/science/biology/bicgl/default.nix
View file

@ -2,21 +2,24 @@
stdenv.mkDerivation rec {
pname = "bicgl";
name = "${pname}-2017-09-10";
version = "unstable-2018-04-06";
owner = "BIC-MNI";
src = fetchFromGitHub {
inherit owner;
repo = pname;
rev = "b7f7e52d1039d6202a93d9055f516186033656cc";
rev = "61a035751c9244fcca1edf94d6566fa2a709ce90";
sha256 = "0lzirdi1mf4yl8srq7vjn746sbydz7h0wjh7wy8gycy6hq04qrg4";
};
nativeBuildInputs = [ cmake ];
buildInputs = [ libminc bicpl freeglut mesa_glu ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBICPL_DIR=${bicpl}/lib" ];
cmakeFlags = [
"-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DBICPL_DIR=${bicpl}/lib"
];
meta = with stdenv.lib; {
homepage = "https://github.com/${owner}/${pname}";

4
pkgs/development/libraries/science/biology/bicpl/default.nix
View file

@ -2,7 +2,7 @@
stdenv.mkDerivation rec {
pname = "bicpl";
name = "${pname}-2017-09-10";
version = "unstable-2017-09-10";
owner = "BIC-MNI";
@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake ];
buildInputs = [ libminc netpbm ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
doCheck = false;
# internal_volume_io.h: No such file or directory

4
pkgs/development/libraries/science/biology/oobicpl/default.nix
View file

@ -2,7 +2,7 @@
stdenv.mkDerivation rec {
pname = "oobicpl";
name = "${pname}-2016-03-02";
version = "unstable-2016-03-02";
owner = "BIC-MNI";
@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake ];
buildInputs = [ libminc bicpl arguments pcre-cpp ];
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib"
cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
"-DBICPL_DIR=${bicpl}/lib"
"-DARGUMENTS_DIR=${arguments}/lib"
"-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ];

75
pkgs/tools/misc/hdf5/1_8.nix
View file

@ -1,75 +0,0 @@
{ stdenv
, fetchurl
, removeReferencesTo
, cpp ? false
, gfortran ? null
, fortran2003 ? false
, zlib ? null
, szip ? null
, mpi ? null
, enableShared ? true
}:
# cpp and mpi options are mutually exclusive
# (--enable-unsupported could be used to force the build)
assert !cpp || mpi == null;
# Need a Fortran compiler for Fortran2003 bindings
assert fortran2003 -> gfortran != null;
# No point splitting version 1.8.18 into multiple outputs.
# The library /lib/libhdf5.so has a reference to gcc-wrapper
let inherit (stdenv.lib) optional optionals; in
stdenv.mkDerivation rec {
version = "1.8.19";
pname = "hdf5";
src = fetchurl {
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${pname}-${version}/src/${pname}-${version}.tar.bz2";
sha256 = "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r" ;
};
passthru = {
mpiSupport = (mpi != null);
inherit mpi;
};
nativeBuildInputs = [ removeReferencesTo ];
buildInputs = []
++ optional (gfortran != null) gfortran
++ optional (szip != null) szip;
propagatedBuildInputs = []
++ optional (zlib != null) zlib
++ optional (mpi != null) mpi;
configureFlags = []
++ optional cpp "--enable-cxx"
++ optional (gfortran != null) "--enable-fortran"
++ optional fortran2003 "--enable-fortran2003"
++ optional (szip != null) "--with-szlib=${szip}"
++ optionals (mpi != null) ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
++ optional enableShared "--enable-shared";
patches = [./bin-mv.patch];
postInstall = ''
find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' +
'';
meta = {
description = "Data model, library, and file format for storing and managing data";
longDescription = ''
HDF5 supports an unlimited variety of datatypes, and is designed for flexible and efficient
I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing
applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and
applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
'';
license = stdenv.lib.licenses.free; # BSD-like
homepage = "https://www.hdfgroup.org/HDF5/";
platforms = stdenv.lib.platforms.unix;
broken = (gfortran != null) && stdenv.isDarwin;
};
}

10
pkgs/top-level/all-packages.nix
View file

@ -4370,12 +4370,6 @@ in
mpi = null;
};
hdf5_1_8 = callPackage ../tools/misc/hdf5/1_8.nix {
gfortran = null;
szip = null;
mpi = null;
};
hdf5-mpi = appendToName "mpi" (hdf5.override {
szip = null;
mpi = pkgs.openmpi;
@ -13927,9 +13921,7 @@ in
libmilter = callPackage ../development/libraries/libmilter { };
libminc = callPackage ../development/libraries/libminc {
hdf5 = hdf5_1_8;
};
libminc = callPackage ../development/libraries/libminc { };
libmirage = callPackage ../misc/emulators/cdemu/libmirage.nix { };