[Debian-med-packaging] Bug#815996: elastix: diff for NMU version 4.8-3.1
Gianfranco Costamagna
locutusofborg at debian.org
Fri Feb 26 13:58:16 UTC 2016
control: tags -1 patch
control: tags -1 pending
Hi, I'm attaching the patch with the bug closed. And I'm uploading on
deferred/7.
cheers,
G.
On Fri, 26 Feb 2016 13:41:32 +0000 (UTC) Gianfranco Costamagna
<costamagnagianfranco at yahoo.it> wrote:
> Package: elastix
> Version: 4.8-3
> Severity: serious
> Justification: FTBFS
>
>
> Dear maintainer,
>
> the elastix package doesn't build anymore against the new ITK4.9.
> I did cherry-pick the patch from upstream and the build was successful.
>
> build error:
> https://launchpadlibrarian.net/243044486/buildlog_ubuntu-xenial-amd64.elastix_4.8-3build1_BUILDING.txt.gz
> the patch is really simple, you can see it below, or just drag it from there
> http://launchpadlibrarian.net/243063499/elastix_4.8-3build1_4.8-3ubuntu1.diff.gz
>
> upstream commits:
> r5140 | kmarstal | 2015-11-16 09:38:55 +0000 (Mon, 16 Nov 2015) | 1 line
>
> r5139 | dpshamonin | 2015-11-13 12:42:05 +0000 (Fri, 13 Nov 2015) | 1 line
>
>
> I'm uploading it to deferred/15 and attaching the debdiff to this email.
> (I'll close this bug in changelog)
-------------- next part --------------
diff -Nru elastix-4.8/debian/changelog elastix-4.8/debian/changelog
--- elastix-4.8/debian/changelog 2016-01-07 12:50:07.000000000 +0100
+++ elastix-4.8/debian/changelog 2016-02-26 14:46:49.000000000 +0100
@@ -1,3 +1,11 @@
+elastix (4.8-3.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * debian/patches/fix-cast-error.patch:
+ fix FTBFS with insighttoolkit4.9 (Closes: #815996).
+
+ -- Gianfranco Costamagna <locutusofborg at debian.org> Fri, 26 Feb 2016 12:54:10 +0100
+
elastix (4.8-3) unstable; urgency=medium
[ Andreas Tille ]
diff -Nru elastix-4.8/debian/patches/fix-cast-error.patch elastix-4.8/debian/patches/fix-cast-error.patch
--- elastix-4.8/debian/patches/fix-cast-error.patch 1970-01-01 01:00:00.000000000 +0100
+++ elastix-4.8/debian/patches/fix-cast-error.patch 2016-02-26 14:39:54.000000000 +0100
@@ -0,0 +1,70 @@
+Description: fix FTBFS because of an overload issue with ITK-4.9
+
+In file included from /«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.h:430:0,
+ from /«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.cxx:19:
+/«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.hxx:194:45: error: call of overloaded 'vnl_math_min(const unsigned int&, int)' is ambiguous
+ const unsigned int movdim = vnl_math_min( this->GetElastix()->MovingDimension, 2 );
+ ^
+In file included from /usr/include/ITK-4.9/itkVector.hxx:21:0,
+ from /usr/include/ITK-4.9/itkVector.h:289,
+ from /usr/include/ITK-4.9/itkPoint.h:23,
+ from /usr/include/ITK-4.9/itkContinuousIndex.h:21,
+ from /usr/include/ITK-4.9/itkImageRegion.h:34,
+ from /usr/include/ITK-4.9/itkImageIORegion.h:24,
+ from /usr/include/ITK-4.9/itkImageIOBase.h:26,
+ from /usr/include/ITK-4.9/itkImageFileReader.h:24,
+ from /«PKGBUILDDIR»/src/Core/Kernel/elxElastixBase.h:39,
+ from /«PKGBUILDDIR»/src/Core/Kernel/elxElastixTemplate.h:21,
+ from /«PKGBUILDDIR»/src/Core/Install/elxIncludes.h:39,
+ from /«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.h:21,
+ from /«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.cxx:19:
+/usr/include/ITK-4.9/vnl/vnl_math.h:567:27: note: candidate: int vnl_math_min(int, int)
+ inline int vnl_math_min(int x, int y) { return (x < y) ? x : y; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:568:27: note: candidate: unsigned int vnl_math_min(unsigned int, unsigned int)
+ inline unsigned int vnl_math_min(unsigned int x, unsigned int y) { return (x < y) ? x : y; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:569:27: note: candidate: long int vnl_math_min(long int, long int)
+ inline long vnl_math_min(long x, long y) { return (x < y) ? x : y; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:570:27: note: candidate: long unsigned int vnl_math_min(long unsigned int, long unsigned int)
+ inline unsigned long vnl_math_min(unsigned long x, unsigned long y) { return (x < y) ? x : y; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:571:27: note: candidate: long long int vnl_math_min(long long int, long long int)
+ inline long long vnl_math_min(long long x, long long y) { return (x < y) ? x : y; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:572:27: note: candidate: long long unsigned int vnl_math_min(long long unsigned int, long long unsigned int)
+ inline unsigned long long vnl_math_min(unsigned long long x, unsigned long long y) { return (x < y) ? x : y; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:573:27: note: candidate: float vnl_math_min(float, float)
+ inline float vnl_math_min(float x, float y) { return (x > y) ? y : x; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:574:27: note: candidate: double vnl_math_min(double, double)
+ inline double vnl_math_min(double x, double y) { return (x > y) ? y : x; }
+ ^
+/usr/include/ITK-4.9/vnl/vnl_math.h:575:27: note: candidate: long double vnl_math_min(long double, long double)
+ inline long double vnl_math_min(long double x, long double y) { return (x > y) ? y : x; }
+ ^
+In file included from /«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.h:430:0,
+ from /«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.cxx:19:
+/«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.hxx: In instantiation of 'void elastix::AdaptiveStochasticGradientDescent<TElastix>::BeforeEachResolution() [with TElastix = elastix::ElastixTemplate<itk::Image<float, 3u>, itk::Image<float, 3u> >]':
+/«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.cxx:21:53: required from here
+/«PKGBUILDDIR»/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.hxx:193:45: error: call of overloaded 'vnl_math_min(const unsigned int&, int)' is ambiguous
+ const unsigned int fixdim = vnl_math_min( this->GetElastix()->FixedDimension, 2 );
+ ^
+r5140 | kmarstal | 2015-11-16 09:38:55 +0000 (Mon, 16 Nov 2015) | 1 line
+r5139 | dpshamonin | 2015-11-13 12:42:05 +0000 (Fri, 13 Nov 2015) | 1 line
+Origin: upstream
+--- elastix-4.8.orig/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.hxx
++++ elastix-4.8/src/Components/Optimizers/AdaptiveStochasticGradientDescent/elxAdaptiveStochasticGradientDescent.hxx
+@@ -190,8 +190,8 @@ AdaptiveStochasticGradientDescent< TElas
+ /** Set the maximum step length: the maximum displacement of a voxel in mm.
+ * Compute default value: mean in-plane spacing of fixed and moving image.
+ */
+- const unsigned int fixdim = vnl_math_min( this->GetElastix()->FixedDimension, 2 );
+- const unsigned int movdim = vnl_math_min( this->GetElastix()->MovingDimension, 2 );
++ const unsigned int fixdim = vnl_math_min( (unsigned int) this->GetElastix()->FixedDimension, (unsigned int) 2 );
++ const unsigned int movdim = vnl_math_min( (unsigned int) this->GetElastix()->MovingDimension, (unsigned int) 2 );
+ double sum = 0.0;
+ for( unsigned int d = 0; d < fixdim; ++d )
+ {
diff -Nru elastix-4.8/debian/patches/series elastix-4.8/debian/patches/series
--- elastix-4.8/debian/patches/series 2015-10-13 15:31:47.000000000 +0200
+++ elastix-4.8/debian/patches/series 2016-02-26 12:53:20.000000000 +0100
@@ -1,3 +1,4 @@
build-static-ann.patch
doxygen_cleanup.patch
doxygen_use_epoch_for_data_if_given.patch
+fix-cast-error.patch
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