[med-svn] [Git][med-team/insighttoolkit][itk-4.y] 6 commits: denoise-build-log.patch: added to reduce size of build logs.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Nov 21 22:20:22 GMT 2022
Étienne Mollier pushed to branch itk-4.y at Debian Med / insighttoolkit
Commits:
eb51a0ad by Étienne Mollier at 2022-07-29T19:31:16+02:00
denoise-build-log.patch: added to reduce size of build logs.
Closes: #977118
- - - - -
62fe100c by Étienne Mollier at 2022-11-21T22:39:10+01:00
d/{control,rules}: revert to build using gcc-11.
Work around test failures occurring only with gcc-12.
- - - - -
7fc77f13 by Étienne Mollier at 2022-11-21T22:40:44+01:00
d/rules: disable python wrappers.
This resolve another failure to build from source, and substancially
reduces the build time, but renders the insighttoolkit4-python3
package useless.
- - - - -
b8f0caef by Étienne Mollier at 2022-11-21T23:04:55+01:00
d/NEWS: inform end users about disable python wrappers.
- - - - -
5982e677 by Étienne Mollier at 2022-11-21T23:06:54+01:00
d/control: remove now empty insighttoolkit4-python3.
- - - - -
88833e58 by Étienne Mollier at 2022-11-21T23:19:45+01:00
update changelog.
- - - - -
6 changed files:
- debian/NEWS
- debian/changelog
- debian/control
- + debian/patches/denoise-build-log.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/NEWS
=====================================
@@ -1,3 +1,17 @@
+insighttoolkit (4.13.3withdata-dfsg2-4) unstable; urgency=medium
+
+ Due to multiple issues as compiler versions went on, the python
+ wrappers provided by insighttoolkit4-python3 are not available
+ anymore. Since ITK4 is not maintained anymore, users of ITK4 are
+ encouraged to migrate to ITK5. Unfortunately python wrappers are
+ not available for insighttoolkit5 neither. People needing them will
+ have to build their own from upstream source code[1] available on
+ ITK website for the time being.
+
+ [1]: https://itk.org/download/
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 21 Nov 2022 22:43:48 +0100
+
insighttoolkit (3.20.0-4) experimental; urgency=low
Language bindings for java, python, and tcl now use the new-style
=====================================
debian/changelog
=====================================
@@ -1,10 +1,19 @@
insighttoolkit4 (4.13.3withdata-dfsg2-4) UNRELEASED; urgency=medium
- NOTE: the package still ftbfs, but due to failing test item.
* d/rules: add -fno-sized-deallocation; fix ftbfs with gcc-12.
- (Closes: #1012950)
-
- -- Étienne Mollier <emollier at debian.org> Mon, 25 Jul 2022 19:49:22 +0200
+ Note the packaging still fails with gcc-12, but due to failing test items.
+ * denoise-build-log.patch: added to reduce a bit the size of build logs.
+ (Closes: #977118)
+ * d/{control,rules}: revert to build using gcc-11.
+ Work around test failures occurring only with gcc-12.
+ * d/rules: disable python wrappers.
+ This resolves another failure to build from source, and substancially
+ reduces the build time, but renders the insighttoolkit4-python3
+ package useless.
+ * d/NEWS: inform end users about the disabled python wrappers.
+ * d/control: remove the now empty insighttoolkit4-python3 package.
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 21 Nov 2022 23:07:35 +0100
insighttoolkit4 (4.13.3withdata-dfsg2-3) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -7,6 +7,8 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
cmake,
+ gcc-11,
+ g++-11,
dh-python,
swig,
castxml (>= 0.3.4-2),
@@ -105,23 +107,23 @@ Description: Image processing toolkit for registration and segmentation - exampl
.
This package contains the source for example programs.
-Package: insighttoolkit4-python3
-Architecture: amd64 i386
-Section: python
-Depends: ${misc:Depends},
- ${shlibs:Depends},
- ${python3:Depends}
-Conflicts: insighttoolkit-python,
- insighttoolkit4-python
-Description: Image processing toolkit for registration and segmentation - Python bindings
- ITK is an open-source software toolkit for performing registration and
- segmentation. Segmentation is the process of identifying and
- classifying data found in a digitally sampled
- representation. Typically the sampled representation is an image
- acquired from such medical instrumentation as CT or MRI
- scanners. Registration is the task of aligning or developing
- correspondences between data. For example, in the medical
- environment, a CT scan may be aligned with a MRI scan in order to
- combine the information contained in both.
- .
- This package contains the Python bindings.
+#Package: insighttoolkit4-python3
+#Architecture: amd64 i386
+#Section: python
+#Depends: ${misc:Depends},
+# ${shlibs:Depends},
+# ${python3:Depends}
+#Conflicts: insighttoolkit-python,
+# insighttoolkit4-python
+#Description: Image processing toolkit for registration and segmentation - Python bindings
+# ITK is an open-source software toolkit for performing registration and
+# segmentation. Segmentation is the process of identifying and
+# classifying data found in a digitally sampled
+# representation. Typically the sampled representation is an image
+# acquired from such medical instrumentation as CT or MRI
+# scanners. Registration is the task of aligning or developing
+# correspondences between data. For example, in the medical
+# environment, a CT scan may be aligned with a MRI scan in order to
+# combine the information contained in both.
+# .
+# This package contains the Python bindings.
=====================================
debian/patches/denoise-build-log.patch
=====================================
@@ -0,0 +1,25 @@
+Description: don't export VCL_TEMPLATE_EXPORT when gcc is in use.
+ The patch remove_gcc_version_test.patch introduces numerous changes, some
+ of which cause a lot of noise in build logs. The present patch tries to
+ carefully work around the issue with minimal changes. Ideally the previous
+ patch, remove_gcc_version_test.patch, could probably be removed, but I'm not
+ sure of potential adverse effects. The issue is not part of ITK5, so this
+ problem will disappear along with ITK4 package.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=977118
+Forwarded: not-needed
+Last-Update: 2022-07-29
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- insighttoolkit.orig/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h
++++ insighttoolkit/Modules/ThirdParty/VNL/src/vxl/vcl/vcl_compiler.h
+@@ -108,7 +108,8 @@
+ // if the compiler doesn't understand "export", we just leave it out.
+ // gcc understands it, but ignore it noisily.
+ // icc understands it, but ignore it noisily.
+-#if !VCL_HAS_EXPORT || defined(VCL_GCC) || defined(VCL_ICC)
++#if !VCL_HAS_EXPORT || defined(VCL_GCC) || defined(VCL_ICC) \
++ || (defined(__GNUC__) && !defined(__ICC))
+ # define VCL_TEMPLATE_EXPORT /* ignore */
+ #else
+ # define VCL_TEMPLATE_EXPORT export
=====================================
debian/patches/series
=====================================
@@ -13,3 +13,4 @@ python3.8.diff
ignore_failing_test.patch
gcc11.patch
python3.10.patch
+denoise-build-log.patch
=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ PYVER := $(shell py3versions -dv)
#ITK is not properly using system provided headers
export DEB_CPPFLAGS_MAINT_APPEND = -I/usr/include/nifti -g1
-ENABLE_PYTHON=1
+ENABLE_PYTHON=0
ifeq ($(DEB_HOST_ARCH),i386)
ENABLE_FFTW=OFF
@@ -29,6 +29,8 @@ endif
export DEB_CXXFLAGS_MAINT_APPEND += -fno-sized-deallocation
CMAKE_FLAGS = \
+ -DCMAKE_C_COMPILER=/usr/bin/${DEB_HOST_GNU_TYPE}-gcc-11 \
+ -DCMAKE_CXX_COMPILER=/usr/bin/${DEB_HOST_GNU_TYPE}-g++-11 \
-DBUILD_EXAMPLES:BOOL=ON \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DBUILD_TESTING:BOOL=ON \
View it on GitLab: https://salsa.debian.org/med-team/insighttoolkit/-/compare/9c720b1eab3fa22399aee9a9dba0bebca4c804a5...88833e58ab7430389162a2143a1d35c82f5ab23f
--
View it on GitLab: https://salsa.debian.org/med-team/insighttoolkit/-/compare/9c720b1eab3fa22399aee9a9dba0bebca4c804a5...88833e58ab7430389162a2143a1d35c82f5ab23f
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