Source: libminc Version: 2.4.07-1 Severity: important Tags: patch -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512
Hi, I am testing the rebuild of every HDF5 reverse dependencies against HDF5 1.14.6+repack-1~exp17 currently in experimental. The main change to the HDF5 packages is not the minor version bump but the toolchain used for the build: I wanted to switch to cmake because I was told by the HDF Group that they will drop the autotools toolchain at some point in the future. My tests report a FTBFS for insighttoolkit5, which I could pinpoint to a change into the libminc-dev package. Please see the details below. # Current libminc situation when built against HDF5 1.14.5+repack-4 in unstable CMakeLists.tst: HDF5_LIBRARY=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so HDF5_LIBRARY_NAME=libm.so This doesn't seem correct ^^ Generated LIBMINCConfig.cmake (installed by libminc-dev): LIBMINC_LIBRARIES=minc2;libm.so;libz.so;m;dl;libnetcdf.so VOLUME_IO_LIBRARIES=minc2;libm.so;libz.so;m;dl;libnetcdf.so EZMINC_LIBRARIES=minc_io;minc2;libm.so;libz.so;m;dl;libnetcdf.so Package insighttoolkit5 builds fine. # libminc built against HDF5 1.14.6+repack-1 in experimental CMakeLists.txt: HDF5_LIBRARY=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so HDF5_LIBRARY_NAME=libhdf5.so This does seem correct ^^ Generated LIBMINCConfig.cmake: LIBMINC_LIBRARIES=minc2;libhdf5.so;libz.so;m;dl;libnetcdf.so VOLUME_IO_LIBRARIES=minc2;libhdf5.so;libz.so;m;dl;libnetcdf.so EZMINC_LIBRARIES=minc_io;minc2;libhdf5.so;libz.so;m;dl;libnetcdf.so But then insighttoolkit5 FTBFS with: /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/insighttoolkit5-k8zAE3/insighttoolkit5-5.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/nifti -g1 -mtune=generic -march=corei7 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wctad-maybe-unsupported -Wstrict-null-sentinel -fno-sized-deallocation -msse2 -Wl,--dependency-file=CMakeFiles/ITKIOMINC.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libITKIOMINC-5.4.so.1 -o ../../../../lib/x86_64-linux-gnu/libITKIOMINC-5.4.so.1 CMakeFiles/ITKIOMINC.dir/itkMINCImageIO.cxx.o CMakeFiles/ITKIOMINC.dir/itkMINCImageIOFactory.cxx.o -L/usr/lib/x86_64-linux-gnu/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu/lib:/build/insighttoolkit5-k8zAE3/insighttoolkit5-5.4.4/BUILD/lib/x86_64-linux-gnu: ../../../../lib/x86_64-linux-gnu/libITKIOImageBase-5.4.so.1 -lminc2 -lhdf5 -lz -lm -ldl -lnetcdf ../../../../lib/x86_64-linux-gnu/libITKCommon-5.4.so.1 ../../../../lib/x86_64-linux-gnu/libitksys-5.4.so.1 ../../../../lib/x86_64-linux-gnu/libITKVNLInstantiation-5.4.so.1 ../../../../lib/x86_64-linux-gnu/libitkvnl_algo-5.4.so.1 ../../../../lib/x86_64-linux-gnu/libitkvnl-5.4.so.1 ../../../../lib/x86_64-linux-gnu/libitkv3p_netlib-5.4.so.1 ../../../../lib/x86_64-linux-gnu/libitkvcl-5.4.so.1 -lm -lm -ldl -Wl,-rpath-link,/build/insighttoolkit5-k8zAE3/insighttoolkit5-5.4.4/BUILD/lib/x86_64-linux-gnu /usr/bin/ld: cannot find -lhdf5: No such file or directory collect2: error: ld returned 1 exit status # Workaround As I understand it, '-lhdf5' is not needed to link against libminc.so. Hence my proposal to remove 'libhdf5.so' from the libminc generated file 'LIBMINCConfig.cmake'. Please see attached debdiff. New Generated LIBMINCConfig.cmake: LIBMINC_LIBRARIES=minc2;libz.so;m;dl;libnetcdf.so VOLUME_IO_LIBRARIES=minc2;libz.so;m;dl;libnetcdf.so EZMINC_LIBRARIES=minc_io;minc2;libz.so;m;dl;libnetcdf.so Note this is very close to the current situation in unstable ^^ Then libminc and insightoolkit5 build fine in both cases: unstable with HDF5 1.14.5+repack-4, and experimental with HDF5 1.14.6+repack-1. Thanks in advance, _g. - -- System Information: Debian Release: 12.0 Architecture: amd64 (x86_64) Kernel: Linux 6.1.0-34-amd64 (SMP w/12 CPU threads; PREEMPT) Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAmkUk7AACgkQ7+hsbH/+ z4P92AgAqIYHW81uMbIhfBnJR5SLzGSxqKPMWhOeR9cpA9WxuI5jAcSToPrnp+D/ PJw7FDXb4+6/qAS4JDC5cy6EfX2uHZOKqlLlWXq4hz15ZvalZaw+kPiF7c5i/HR1 9FeyHs4kWVX8MaLw2ZNE3eoMXUjPkF71qu7NVvNu9ILLy0qWGoKXct6wBVTC8ZFJ VFj4sXQS1+kz7Mt+V2qN84kBmrsoGB4Viaj/HGGU7CHw5CV0XGDcttG7d8mKVNPo js1lPM3mJihj9icCsl82yhdwAarq23o5/EzSJ8Hbpc7E5vsim1CYP+SSczJURZEh zFaKXa3DDfH/m0CfRIpp/gMiJ191pg== =g5U7 -----END PGP SIGNATURE-----
diff -Nru libminc-2.4.07/debian/changelog libminc-2.4.07/debian/changelog --- libminc-2.4.07/debian/changelog 2025-10-24 02:28:01.000000000 +0200 +++ libminc-2.4.07/debian/changelog 2025-11-12 10:24:52.000000000 +0100 @@ -1,3 +1,11 @@ +libminc (2.4.07-1.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * New patch to drop libhdf5.so from LIBMINC_LIBRARIES_CONFIG + (fix FTBFS for insighttoolkit5 against HDF5 1.14.6 built with cmake) + + -- Gilles Filippini <[email protected]> Wed, 12 Nov 2025 10:24:52 +0100 + libminc (2.4.07-1) unstable; urgency=medium [ Steve M. Robbins ] diff -Nru libminc-2.4.07/debian/patches/0006-Drop-hdf5-from_LIBMINC_LIBRARIES_CONFIG.patch libminc-2.4.07/debian/patches/0006-Drop-hdf5-from_LIBMINC_LIBRARIES_CONFIG.patch --- libminc-2.4.07/debian/patches/0006-Drop-hdf5-from_LIBMINC_LIBRARIES_CONFIG.patch 1970-01-01 01:00:00.000000000 +0100 +++ libminc-2.4.07/debian/patches/0006-Drop-hdf5-from_LIBMINC_LIBRARIES_CONFIG.patch 2025-11-12 10:24:52.000000000 +0100 @@ -0,0 +1,15 @@ +Index: libminc-2.4.07/CMakeLists.txt +=================================================================== +--- libminc-2.4.07.orig/CMakeLists.txt ++++ libminc-2.4.07/CMakeLists.txt +@@ -425,8 +425,8 @@ ENDIF() + get_filename_component(HDF5_LIBRARY_NAME "${HDF5_LIBRARY}" NAME) + get_filename_component(ZLIB_LIBRARY_NAME "${ZLIB_LIBRARY}" NAME) + +-SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARY} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY}) +-SET(LIBMINC_LIBRARIES_CONFIG ${LIBMINC_LIBRARY} ${HDF5_LIBRARY_NAME} ${NIFTI_LIBRARY_NAME} ${ZNZ_LIBRARY_NAME} ${ZLIB_LIBRARY_NAME}) ++SET(LIBMINC_LIBRARIES ${LIBMINC_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY}) ++SET(LIBMINC_LIBRARIES_CONFIG ${LIBMINC_LIBRARY} ${NIFTI_LIBRARY_NAME} ${ZNZ_LIBRARY_NAME} ${ZLIB_LIBRARY_NAME}) + message("LIBMINC_LIBRARIES_CONFIG=${LIBMINC_LIBRARIES_CONFIG}") + + SET(LIBMINC_STATIC_LIBRARIES ${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY}) diff -Nru libminc-2.4.07/debian/patches/series libminc-2.4.07/debian/patches/series --- libminc-2.4.07/debian/patches/series 2025-10-24 02:28:01.000000000 +0200 +++ libminc-2.4.07/debian/patches/series 2025-11-12 10:24:52.000000000 +0100 @@ -3,3 +3,4 @@ 0003-disable-dimension-test.patch 0004-Fix-setting-of-LIBMINC_USE_FILE_CONFIG-to-be-correct.patch 0005-Disable-setting-RPATH.patch +0006-Drop-hdf5-from_LIBMINC_LIBRARIES_CONFIG.patch
