[med-svn] [Git][med-team/minc-tools][master] 5 commits: Fix CMake patch Closes: #1136921
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat May 30 09:16:09 BST 2026
Andreas Tille pushed to branch master at Debian Med / minc-tools
Commits:
37f9ade2 by Andreas Tille at 2026-05-30T08:45:18+02:00
Fix CMake patch Closes: #1136921
- - - - -
610f33ad by Andreas Tille at 2026-05-30T08:45:42+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
4498f559 by Andreas Tille at 2026-05-30T08:45:58+02:00
debputy lint --auto-fix (routine-update)
- - - - -
e4984b88 by Andreas Tille at 2026-05-30T10:06:34+02:00
Fix CMake patch and adapt to latest CMake
- - - - -
c5fd3689 by Andreas Tille at 2026-05-30T10:09:46+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/cmake_4.2.patch
- + debian/patches/ignore_local_cmake_findhdf5.patch
- debian/patches/series
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+minc-tools (2.3.00+dfsg-17) unstable; urgency=medium
+
+ * Fix CMake patch and adapt to latest CMake
+ Closes: #1136921
+ * Standards-Version: 4.7.4 (routine-update)
+ * debputy lint --auto-fix (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sat, 30 May 2026 10:06:54 +0200
+
minc-tools (2.3.00+dfsg-16) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,5 +1,5 @@
Source: minc-tools
-Standards-Version: 4.7.3
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders:
Steve M. Robbins <smr at debian.org>,
@@ -11,6 +11,7 @@ Build-Depends:
bison,
flex,
libminc-dev,
+ libhdf5-dev,
libnifti2-dev,
libnetcdf-dev,
zlib1g-dev,
=====================================
debian/patches/cmake_4.2.patch
=====================================
@@ -7,7 +7,15 @@ Last-Update: 2026-02-22
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -17,13 +17,7 @@
+@@ -3,6 +3,7 @@
+ # Andrew Janke - a.janke at gmail.com
+ # Vladimir S. FONOV - vladimir.fonov at gmail.com
+
++CMAKE_MINIMUM_REQUIRED(VERSION 4.2)
+ PROJECT(minc-tools)
+
+ SET(MINC_TOOLS_PACKAGE_VERSION_MAJOR 2)
+@@ -17,13 +18,6 @@ SET(PACKAGE_STRING "${PACKAGE_NAME} ${P
ENABLE_TESTING()
INCLUDE(CTest)
@@ -18,7 +26,6 @@ Last-Update: 2026-02-22
- CMAKE_POLICY(SET CMP0026 OLD) # NEEDED in testing to read location of target
- ENDIF(POLICY CMP0026)
-ENDIF(COMMAND CMAKE_POLICY)
-+CMAKE_MINIMUM_REQUIRED(VERSION 4.2)
IF(MINC_TOOLKIT_BUILD)
SET(MINC_TOOLS_EXTERNALLY_CONFIGURED ON)
@@ -49,7 +56,7 @@ Last-Update: 2026-02-22
# Copy files used by minccalc-test and other tests.
CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/test-zero.mnc" "${CMAKE_CURRENT_BINARY_DIR}/test-zero.mnc" COPYONLY)
-@@ -42,7 +42,7 @@
+@@ -42,7 +42,7 @@ SET_TESTS_PROPERTIES(mincaverage-test
PROPERTIES ENVIRONMENT "MINCAVERAGE_BIN=${mincaverage_bin};MINCSTATS_BIN=${mincstats_bin}")
# Get path to the binary.
@@ -58,7 +65,7 @@ Last-Update: 2026-02-22
# Add the test.
ADD_TEST(minccalc-test ${CMAKE_CURRENT_SOURCE_DIR}/minccalc-test.sh)
-@@ -59,7 +59,7 @@
+@@ -59,7 +59,7 @@ SET_TESTS_PROPERTIES(mincresample-test
PROPERTIES ENVIRONMENT "MINCRESAMPLE_BIN=${mincresample_bin};MINCSTATS_BIN=${mincstats_bin}")
# Get path to mincaverage binary.
=====================================
debian/patches/ignore_local_cmake_findhdf5.patch
=====================================
@@ -0,0 +1,109 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-05-30
+Bug-Debian: https://bugs.debian.org/1136921
+Description: Make sure package builds with latest CMake
+
+--- a/cmake-modules/FindHDF5.cmake
++++ /dev/null
+@@ -1,81 +0,0 @@
+-#
+-# this module look for HDF5 (http://hdf.ncsa.uiuc.edu) support
+-# it will define the following values
+-#
+-# HDF5_INCLUDE_DIR = where hdf5.h can be found
+-# HDF5_LIBRARY = the library to link against (hdf5 etc)
+-# HDF5_FOUND = set to true after finding the library
+-#
+-
+-IF(EXISTS ${PROJECT_CMAKE}/Hdf5Config.cmake)
+- INCLUDE(${PROJECT_CMAKE}/Hdf5Config.cmake)
+-ENDIF(EXISTS ${PROJECT_CMAKE}/Hdf5Config.cmake)
+-
+-IF(Hdf5_INCLUDE_DIRS)
+-
+- FIND_PATH(HDF5_INCLUDE_DIR hdf5.h ${Hdf5_INCLUDE_DIRS})
+- FIND_LIBRARY(HDF5_LIBRARY hdf5 ${Hdf5_LIBRARY_DIRS})
+-
+-ELSE(Hdf5_INCLUDE_DIRS)
+-
+- SET(TRIAL_LIBRARY_PATHS
+- $ENV{HDF5_HOME}/lib
+- /usr/apps/lib
+- /usr/lib
+- /usr/local/lib
+- /opt/lib
+- /sw/lib
+- )
+-
+- SET(TRIAL_INCLUDE_PATHS
+- $ENV{HDF5_HOME}/include
+- /usr/apps/include
+- /usr/include
+- /opt/include
+- /usr/local/include
+- /sw/include
+- )
+-
+- IF($ENV{HDF5_DIR} MATCHES "hdf")
+- MESSAGE(STATUS "Using environment variable HDF5_DIR.")
+- SET(TRIAL_LIBRARY_PATHS $ENV{HDF5_DIR}/lib ${TRIAL_LIBRARY_PATHS} )
+- SET(TRIAL_INCLUDE_PATHS $ENV{HDF5_DIR}/include ${TRIAL_INCLUDE_PATHS} )
+- ENDIF($ENV{HDF5_DIR} MATCHES "hdf")
+-
+- FIND_LIBRARY(HDF5_LIBRARY hdf5 ${TRIAL_LIBRARY_PATHS})
+- FIND_PATH(HDF5_INCLUDE_DIR hdf5.h ${TRIAL_INCLUDE_PATHS} )
+-
+-ENDIF(Hdf5_INCLUDE_DIRS)
+-
+-## -----------------------------------------------------------------------------
+-## Assign status of the search
+-
+-IF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
+- SET(HDF5_FOUND 1 CACHE BOOL "Found hdf5 library")
+-ELSE(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
+- SET(HDF5_FOUND 0 CACHE BOOL "Not fount hdf5 library")
+-ENDIF(HDF5_INCLUDE_DIR AND HDF5_LIBRARY)
+-
+-## -----------------------------------------------------------------------------
+-## Feedback
+-
+-IF (HDF5_FOUND)
+- IF (NOT HDF5_FIND_QUIETLY)
+- MESSAGE (STATUS "Found components for HDF5")
+- MESSAGE (STATUS "HDF5 library : ${HDF5_LIBRARY}")
+- MESSAGE (STATUS "HDF5 headers : ${HDF5_INCLUDE_DIR}")
+- ENDIF (NOT HDF5_FIND_QUIETLY)
+-ELSE (HDF5_FOUND)
+- IF (HDF5_FIND_REQUIRED)
+- MESSAGE (FATAL_ERROR "Could not find HDF5!")
+- ENDIF (HDF5_FIND_REQUIRED)
+-ENDIF (HDF5_FOUND)
+-
+-## -----------------------------------------------------------------------------
+-## Variables marked as advanced
+-
+-MARK_AS_ADVANCED(
+- HDF5_INCLUDE_DIR
+- HDF5_LIBRARY
+- HDF5_FOUND
+-)
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -37,7 +37,16 @@ IF(NOT MINC_TOOLS_EXTERNALLY_CONFIGURED)
+
+ ENDIF(NOT MINC_TOOLS_EXTERNALLY_CONFIGURED)
+
+-INCLUDE( ${LIBMINC_USE_FILE} )
++FIND_FILE(_libminc_use_file UseLIBMINC.cmake
++ PATHS /usr/lib/${CMAKE_LIBRARY_ARCHITECTURE}/cmake/LIBMINC
++ /usr/share/cmake/LIBMINC
++ ${LIBMINC_DIR}
++ NO_DEFAULT_PATH)
++IF(_libminc_use_file)
++ INCLUDE(${_libminc_use_file})
++ELSE()
++ INCLUDE(${LIBMINC_USE_FILE})
++ENDIF()
+ INCLUDE( InstallManPages )
+ # check for prereqs
+ INCLUDE(CheckFunctionExists)
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ fix-gcc10-build.patch
mnc2nii-use-size-t.patch
netcdf-4.9.3.patch
cmake_4.2.patch
+ignore_local_cmake_findhdf5.patch
=====================================
debian/rules
=====================================
@@ -26,7 +26,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
dh $@
override_dh_auto_configure:
- dh_auto_configure -- $(CMAKE_FLAGS)
+ dh_auto_configure -- $(CMAKE_FLAGS) -DCMAKE_POLICY_VERSION_MINIMUM=3.5
override_dh_install:
cd debian/minc-tools && mkdir -p usr/share && mv usr/man usr/share
=====================================
debian/watch
=====================================
@@ -3,6 +3,6 @@ Version: 5
Template: Github
Owner: BIC-MNI
Project: minc-tools
-Dversionmangle: auto
-Repacksuffix: +dfsg
-Uversionmangle: s/-/./g
+Dversion-Mangle: auto
+Repack-Suffix: +dfsg
+Uversion-Mangle: s/-/./g
View it on GitLab: https://salsa.debian.org/med-team/minc-tools/-/compare/affce6faba8b43f9819296917cc6026cce9eb208...c5fd3689766d2bde40dcd8162f5f20e8cad82db3
--
View it on GitLab: https://salsa.debian.org/med-team/minc-tools/-/compare/affce6faba8b43f9819296917cc6026cce9eb208...c5fd3689766d2bde40dcd8162f5f20e8cad82db3
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