From 54ef40a1f79d6d636ba26ac47f6dd0b84172dd0d Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer Date: Fri, 13 May 2022 11:47:19 -0400 Subject: gnu: mia: Update to 2.4.7. * gnu/packages/patches/mia-fix-boost-headers.patch: New patch. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/image-processing.scm (mia): Update to 2.4.7. [source]: Apply patch. [configure-flags]: Use the more conventional OFF option value (instead of 0). [inputs]: Use new style. Replace python2-lxml by python-lxml. Replace vtk by vtk-7. [native-inputs]: Use new style. Replace python-2 with python-wrapper. --- gnu/local.mk | 1 + gnu/packages/image-processing.scm | 56 +-- gnu/packages/patches/mia-fix-boost-headers.patch | 479 +++++++++++++++++++++++ 3 files changed, 510 insertions(+), 26 deletions(-) create mode 100644 gnu/packages/patches/mia-fix-boost-headers.patch diff --git a/gnu/local.mk b/gnu/local.mk index c4d774052b..83ee7e2930 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1492,6 +1492,7 @@ dist_patch_DATA = \ %D%/packages/patches/mesa-skip-tests.patch \ %D%/packages/patches/meson-allow-dirs-outside-of-prefix.patch \ %D%/packages/patches/mhash-keygen-test-segfault.patch \ + %D%/packages/patches/mia-fix-boost-headers.patch \ %D%/packages/patches/minetest-add-MINETEST_MOD_PATH.patch \ %D%/packages/patches/mingw-w64-6.0.0-gcc.patch \ %D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch \ diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index e725fe04f7..f4bf1724b4 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -185,7 +185,7 @@ licences similar to the Modified BSD licence.")))) (define-public mia (package (name "mia") - (version "2.4.6") + (version "2.4.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/mia/mia/" @@ -193,37 +193,41 @@ licences similar to the Modified BSD licence.")))) "/mia-" version ".tar.xz")) (sha256 (base32 - "0j4nd5z7i3v199jh7hqqhwd4g7snchizkc7rhzanpvngqg91m1pb")))) + "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1")) + (patches (search-patches "mia-fix-boost-headers.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags - (list "-DMIA_CREATE_NIPYPE_INTERFACES=0" + (list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF" "-DCMAKE_CXX_FLAGS=-fpermissive"))) (inputs - `(("boost" ,boost) - ("dcmtk" ,dcmtk) - ("doxygen" ,doxygen) - ("eigen" ,eigen) - ("fftw" ,fftw) - ("fftwf" ,fftwf) - ("gsl" ,gsl) - ("gts" ,gts) - ("hdf5" ,hdf5) - ("itpp" ,itpp) - ("libjpeg" ,libjpeg-turbo) - ("libpng" ,libpng) - ("libtiff" ,libtiff) - ("libxml" ,libxml2) - ("libxml++" ,libxml++) - ("maxflow" ,maxflow) - ("niftilib" ,niftilib) - ("nlopt" ,nlopt) - ("openexr" ,openexr-2) - ("python-lxml" ,python2-lxml) - ("vtk" ,vtk))) + (list boost + dcmtk + doxygen + eigen + fftw + fftwf + gsl + gts + hdf5 + itpp + libjpeg-turbo + libpng + libtiff + libxml2 + libxml++ + maxflow + niftilib + nlopt + openexr-2 + python-lxml + ;; The build fails when using the regular VTK (currently at version + ;; 9), with error "addons/vtk/vtkvf.cc:23:10: fatal error: + ;; vtkStructuredPointsReader.h: No such file or directory". + vtk-7)) (native-inputs - `(("pkg-config" ,pkg-config) - ("python" ,python-2))) + (list pkg-config + python-wrapper)) (home-page "http://mia.sourceforge.net") (synopsis "Toolkit for gray scale medical image analysis") (description "MIA provides a combination of command line tools, plug-ins, diff --git a/gnu/packages/patches/mia-fix-boost-headers.patch b/gnu/packages/patches/mia-fix-boost-headers.patch new file mode 100644 index 0000000000..158ab2afeb --- /dev/null +++ b/gnu/packages/patches/mia-fix-boost-headers.patch @@ -0,0 +1,479 @@ +Retrieved from Debian, and added a few "#include " +directives to fix the build. + +diff --git a/addons/hdf5/test_hdf5_3dimage.cc b/addons/hdf5/test_hdf5_3dimage.cc +index a7185618..7a398821 100644 +--- a/addons/hdf5/test_hdf5_3dimage.cc ++++ b/addons/hdf5/test_hdf5_3dimage.cc +@@ -23,7 +23,7 @@ + #include + + #include +-#include ++#include + + #include + +diff --git a/addons/hdf5/test_hdf5mia.cc b/addons/hdf5/test_hdf5mia.cc +index 3d62106e..8141be07 100644 +--- a/addons/hdf5/test_hdf5mia.cc ++++ b/addons/hdf5/test_hdf5mia.cc +@@ -23,7 +23,6 @@ + #include + + #include +-#include + #include + + #include +diff --git a/addons/nifti/test_niftiimage.cc b/addons/nifti/test_niftiimage.cc +index 8df3f0b5..840ae585 100644 +--- a/addons/nifti/test_niftiimage.cc ++++ b/addons/nifti/test_niftiimage.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/addons/vistaio/test_2dvistaio.cc b/addons/vistaio/test_2dvistaio.cc +index b3da29a0..9b1599dd 100644 +--- a/addons/vistaio/test_2dvistaio.cc ++++ b/addons/vistaio/test_2dvistaio.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/addons/vistaio/test_3dvistaio.cc b/addons/vistaio/test_3dvistaio.cc +index 93c007d0..c3ae1fdb 100644 +--- a/addons/vistaio/test_3dvistaio.cc ++++ b/addons/vistaio/test_3dvistaio.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/addons/vtk/test_vtkimage.cc b/addons/vtk/test_vtkimage.cc +index eaf96a6b..8212ef1d 100644 +--- a/addons/vtk/test_vtkimage.cc ++++ b/addons/vtk/test_vtkimage.cc +@@ -23,8 +23,6 @@ + #include + + #include +-#include +- + + #include + #include +diff --git a/mia/2d/creator/test_circle.cc b/mia/2d/creator/test_circle.cc +index 9784e05d..7ca4bab9 100644 +--- a/mia/2d/creator/test_circle.cc ++++ b/mia/2d/creator/test_circle.cc +@@ -21,8 +21,6 @@ + + #include + #include +-#include +- + #include + + using namespace mia; +diff --git a/mia/2d/filter/test_convert.cc b/mia/2d/filter/test_convert.cc +index 80304793..f40d295a 100644 +--- a/mia/2d/filter/test_convert.cc ++++ b/mia/2d/filter/test_convert.cc +@@ -25,7 +25,6 @@ + #include + + #include +-#include + #include + + +diff --git a/mia/2d/filter/test_morphological.cc b/mia/2d/filter/test_morphological.cc +index 2fc58583..9a004946 100644 +--- a/mia/2d/filter/test_morphological.cc ++++ b/mia/2d/filter/test_morphological.cc +@@ -20,7 +20,6 @@ + + #include + #include +-#include + #include + + namespace bmpl = boost::mpl; +diff --git a/mia/2d/filter/test_sortlabel.cc b/mia/2d/filter/test_sortlabel.cc +index 78464e1a..49c327e3 100644 +--- a/mia/2d/filter/test_sortlabel.cc ++++ b/mia/2d/filter/test_sortlabel.cc +@@ -23,7 +23,6 @@ + #include + + #include +-#include + namespace bmpl = boost::mpl; + + +diff --git a/mia/2d/filter/test_thinning.cc b/mia/2d/filter/test_thinning.cc +index 3ebb2cdc..8bc5b356 100644 +--- a/mia/2d/filter/test_thinning.cc ++++ b/mia/2d/filter/test_thinning.cc +@@ -21,7 +21,6 @@ + + #include + #include +-#include + #include + #include + +diff --git a/mia/2d/test_filter_cast.cc b/mia/2d/test_filter_cast.cc +index e806e14f..91c77398 100644 +--- a/mia/2d/test_filter_cast.cc ++++ b/mia/2d/test_filter_cast.cc +@@ -24,7 +24,7 @@ + #include + #include + +-#include ++#include + #include + #include + +diff --git a/mia/2d/test_image.cc b/mia/2d/test_image.cc +index c82dc59b..1f602510 100644 +--- a/mia/2d/test_image.cc ++++ b/mia/2d/test_image.cc +@@ -24,6 +24,7 @@ + #include + + #include ++#include + + #include + +diff --git a/mia/2d/test_interpol.cc b/mia/2d/test_interpol.cc +index d1f3703d..5caafccf 100644 +--- a/mia/2d/test_interpol.cc ++++ b/mia/2d/test_interpol.cc +@@ -23,7 +23,6 @@ + + #include + +-#include + #include + #include + +diff --git a/mia/3d/fifotestfixture.cc b/mia/3d/fifotestfixture.cc +index ab2e7c65..1b6e6bb4 100644 +--- a/mia/3d/fifotestfixture.cc ++++ b/mia/3d/fifotestfixture.cc +@@ -24,7 +24,7 @@ + + #include + #include +-#include ++#include + #include + #include + #include +diff --git a/mia/3d/filter/test_convert.cc b/mia/3d/filter/test_convert.cc +index e83032c1..dad9afaa 100644 +--- a/mia/3d/filter/test_convert.cc ++++ b/mia/3d/filter/test_convert.cc +@@ -20,7 +20,6 @@ + + #include + #include +-#include + #include + #include + #include +diff --git a/mia/3d/test_image.cc b/mia/3d/test_image.cc +index 18f71892..c21e0d20 100644 +--- a/mia/3d/test_image.cc ++++ b/mia/3d/test_image.cc +@@ -21,7 +21,8 @@ + #include + #include + #include +-#include ++#include ++#include + + #include + #include +diff --git a/mia/3d/test_imageio.cc b/mia/3d/test_imageio.cc +index 0640a668..7a6b5635 100644 +--- a/mia/3d/test_imageio.cc ++++ b/mia/3d/test_imageio.cc +@@ -20,7 +20,6 @@ + + #include + #include +-#include + #include + + #include +diff --git a/mia/core/splinekernel/test_bspline.cc b/mia/core/splinekernel/test_bspline.cc +index 54d6bda3..0abfe443 100644 +--- a/mia/core/splinekernel/test_bspline.cc ++++ b/mia/core/splinekernel/test_bspline.cc +@@ -23,8 +23,6 @@ + #include + #include + #include +-#include +- + + using namespace mia; + using namespace mia::bsplinekernel; +diff --git a/mia/core/test_cost.cc b/mia/core/test_cost.cc +index 70097b2e..305ca84d 100644 +--- a/mia/core/test_cost.cc ++++ b/mia/core/test_cost.cc +@@ -27,7 +27,7 @@ + #include + + #include +-#include ++#include + #include + + NS_MIA_USE +diff --git a/mia/core/test_cstplan.cc b/mia/core/test_cstplan.cc +index aa241d48..a9e5a0e3 100644 +--- a/mia/core/test_cstplan.cc ++++ b/mia/core/test_cstplan.cc +@@ -23,7 +23,7 @@ + + #include + #include +-#include ++#include + + #include + +diff --git a/mia/core/test_dictmap.cc b/mia/core/test_dictmap.cc +index a9217290..fd05fe30 100644 +--- a/mia/core/test_dictmap.cc ++++ b/mia/core/test_dictmap.cc +@@ -26,7 +26,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_fifofilter.cc b/mia/core/test_fifofilter.cc +index 2a066f2e..6e2a385d 100644 +--- a/mia/core/test_fifofilter.cc ++++ b/mia/core/test_fifofilter.cc +@@ -27,7 +27,7 @@ + + #include + #include +-#include ++#include + + + #include +diff --git a/mia/core/test_gsl_matrix.cc b/mia/core/test_gsl_matrix.cc +index 4add5f7a..6d16353d 100644 +--- a/mia/core/test_gsl_matrix.cc ++++ b/mia/core/test_gsl_matrix.cc +@@ -25,7 +25,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + #include + + #include +diff --git a/mia/core/test_gsl_matrix_vector_ops.cc b/mia/core/test_gsl_matrix_vector_ops.cc +index e5f7d7b9..217020f7 100644 +--- a/mia/core/test_gsl_matrix_vector_ops.cc ++++ b/mia/core/test_gsl_matrix_vector_ops.cc +@@ -28,7 +28,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_gsl_multimin.cc b/mia/core/test_gsl_multimin.cc +index 5bbc434b..129f578a 100644 +--- a/mia/core/test_gsl_multimin.cc ++++ b/mia/core/test_gsl_multimin.cc +@@ -25,7 +25,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + #include + + #include +diff --git a/mia/core/test_gsl_pca.cc b/mia/core/test_gsl_pca.cc +index 436b36b0..12942921 100644 +--- a/mia/core/test_gsl_pca.cc ++++ b/mia/core/test_gsl_pca.cc +@@ -27,7 +27,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + + #include + +diff --git a/mia/core/test_gsl_vector.cc b/mia/core/test_gsl_vector.cc +index 541c88b8..ba91f159 100644 +--- a/mia/core/test_gsl_vector.cc ++++ b/mia/core/test_gsl_vector.cc +@@ -25,10 +25,9 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_ALTERNATIVE_INIT_API + #include +-#include ++#include + + #include +-#include + + #include + +diff --git a/mia/core/test_interpol.cc b/mia/core/test_interpol.cc +index 36669dc0..2dd5157d 100644 +--- a/mia/core/test_interpol.cc ++++ b/mia/core/test_interpol.cc +@@ -24,7 +24,7 @@ + #include + + #include +-#include ++#include + #include + #include + +diff --git a/mia/core/test_parameter.cc b/mia/core/test_parameter.cc +index ae9b4976..28ef2a80 100644 +--- a/mia/core/test_parameter.cc ++++ b/mia/core/test_parameter.cc +@@ -26,7 +26,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_probmap.cc b/mia/core/test_probmap.cc +index 2dc6cb6c..38052681 100644 +--- a/mia/core/test_probmap.cc ++++ b/mia/core/test_probmap.cc +@@ -22,7 +22,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/mia/core/test_sqmin.cc b/mia/core/test_sqmin.cc +index f00b3b85..4a0b67b9 100644 +--- a/mia/core/test_sqmin.cc ++++ b/mia/core/test_sqmin.cc +@@ -23,7 +23,7 @@ + #define BOOST_TEST_DYN_LINK + #include + #include +-#include ++#include + + #include + +diff --git a/mia/internal/autotest.hh b/mia/internal/autotest.hh +index 419f6e8f..4458c0b2 100644 +--- a/mia/internal/autotest.hh ++++ b/mia/internal/autotest.hh +@@ -34,7 +34,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_NO_MAIN + #include +-#include ++#include + + #include + #include +diff --git a/mia/internal/plugintester.hh b/mia/internal/plugintester.hh +index 2d42b858..e632e5f7 100644 +--- a/mia/internal/plugintester.hh ++++ b/mia/internal/plugintester.hh +@@ -31,7 +31,7 @@ + #define BOOST_TEST_MAIN + #define BOOST_TEST_NO_MAIN + #include +-#include ++#include + + #include + #include +diff --git a/mia/test/testhelpers.hh b/mia/test/testhelpers.hh +index 27f37e7f..68c213a6 100644 +--- a/mia/test/testhelpers.hh ++++ b/mia/test/testhelpers.hh +@@ -23,7 +23,7 @@ + + #include + #include +-#include ++#include + + namespace miatest + { +diff --git a/src/2dlerp.cc b/src/2dlerp.cc +index 4c7dde77..1e8801de 100644 +--- a/src/2dlerp.cc ++++ b/src/2dlerp.cc +@@ -25,7 +25,7 @@ + + #include + #include +-#include ++#include + + #include + #include +diff --git a/src/3dlerp.cc b/src/3dlerp.cc +index 6ee8dca0..2f1c1f3a 100644 +--- a/src/3dlerp.cc ++++ b/src/3dlerp.cc +@@ -24,7 +24,7 @@ + #define BOOST_TEST_NO_MAIN + #include + #include +-#include ++#include + + #include + #include -- cgit v1.2.3