Your message dated Mon, 17 Nov 2025 17:55:52 +0000
with message-id <[email protected]>
and subject line Bug#1120574: fixed in libminc 2.4.07-2
has caused the Debian Bug report #1120574,
regarding libminc: Support for cmake built HDF5 - Fix insighttoolkit5 FTBFS
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1120574: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1120574
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
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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
--- End Message ---
--- Begin Message ---
Source: libminc
Source-Version: 2.4.07-2
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libminc, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated libminc package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 17 Nov 2025 18:15:17 +0100
Source: libminc
Architecture: source
Version: 2.4.07-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1120574
Changes:
libminc (2.4.07-2) unstable; urgency=medium
.
[ Gilles Filippini ]
* New patch to drop libhdf5.so from LIBMINC_LIBRARIES_CONFIG
(fix FTBFS for insighttoolkit5 against HDF5 1.14.6 built with cmake)
Closes: #1120574
.
[ Andreas Tille ]
* d/watch: Version=5
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