Bug#853599: [Debian-med-packaging] Bug#853599: opensurgsim: ftbfs with GCC-7
On Wed, Dec 6, 2017, at 11:28 AM, Andreas Tille wrote: > On Wed, Dec 06, 2017 at 04:51:17PM +0100, Fabian Klötzl wrote: > > // TODO(bert): There is some Eigen flag that causes matrices and > > vectors> > to be > > // initialized after all! We should check for that here. > > > > So I am guessing that the authors knew that their test was flaky and> > > > thus we should be save deactivating them. If you agree, I will go > > ahead.> > Sounds sensible - so I agree. :-) > > An information to upstream that we skip the test and by doing so > informing them that it really causes problems in a practical > application> would complete the work on the bug. > > Kind regards > > Andreas. > > -- > http://fam-tille.de > Sorry again for not looking at this. These tests appear to be from the Unit Tests that test Eigen and not really opensurgsim. I think they can all be safely disabled, since we can trust that Eigen works. These failures are mostly floating point errors. So yes Fabian, please go ahead and disable them. If you want to just disable them all, I think if you set BUILD_TESTING_EIGEN to OFF on line 29 in Debian/rules, you should solve this and other future issues.
Bug#853599: opensurgsim: ftbfs with GCC-7
Hi Andreas, sorry about my radio silence. I'll take a look. -Paul On Wed, Sep 20, 2017, at 03:56 AM, Andreas Tille wrote: > Hi Paul, > > that's the last open gcc-7 bug of the Debian Med team. Could you please > have a look (or at least signal that you will not be able to care about > it)? > > Kind regards > > Andreas. > > On Tue, Jan 31, 2017 at 09:34:51AM +, Matthias Klose wrote: > > Package: src:opensurgsim > > Version: 0.7.0-5 > > Severity: normal > > Tags: sid buster > > User: debian-...@lists.debian.org > > Usertags: ftbfs-gcc-7 > > > > Please keep this issue open in the bug tracker for the package it > > was filed for. If a fix in another package is required, please > > file a bug for the other package (or clone), and add a block in this > > package. Please keep the issue open until the package can be built in > > a follow-up test rebuild. > > > > The package fails to build in a test rebuild on at least amd64 with > > gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The > > severity of this report may be raised before the buster release. > > There is no need to fix this issue in time for the stretch release. > > > > The full build log can be found at: > > http://people.debian.org/~doko/logs/gcc7-20170126/opensurgsim_0.7.0-5_unstable_gcc7.log > > The last lines of the build log are at the end of this report. > > > > To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly, > > or install the gcc, g++, gfortran, ... packages from experimental. > > > > apt-get -t=experimental install g++ > > > > Common build failures are new warnings resulting in build failures with > > -Werror turned on, or new/dropped symbols in Debian symbols files. > > For other C/C++ related build failures see the porting guide at > > http://gcc.gnu.org/gcc-7/porting_to.html > > > > [...] > > [ RUN ] AllDynamicVectorTests/2.addSubVector > > [ OK ] AllDynamicVectorTests/2.addSubVector (0 ms) > > [ RUN ] AllDynamicVectorTests/2.addSubVectorBlocks > > [ OK ] AllDynamicVectorTests/2.addSubVectorBlocks (0 ms) > > [ RUN ] AllDynamicVectorTests/2.setSubVector > > [ OK ] AllDynamicVectorTests/2.setSubVector (1 ms) > > [ RUN ] AllDynamicVectorTests/2.getSubVector > > [ OK ] AllDynamicVectorTests/2.getSubVector (0 ms) > > [ RUN ] AllDynamicVectorTests/2.getSubVectorBlocks > > [ OK ] AllDynamicVectorTests/2.getSubVectorBlocks (0 ms) > > [--] 6 tests from AllDynamicVectorTests/2 (1 ms total) > > > > [--] Global test environment tear-down > > [==] 896 tests from 116 test cases ran. (7703 ms total) > > [ PASSED ] 889 tests. > > [ FAILED ] 7 tests, listed below: > > [ FAILED ] UnalignedMatrixTests/0.DefaultConstructorInitialization, where > > TypeParam = Eigen::Matrix > > [ FAILED ] UnalignedMatrixTests/2.DefaultConstructorInitialization, where > > TypeParam = Eigen::Matrix > > [ FAILED ] UnalignedMatrixTests/3.DefaultConstructorInitialization, where > > TypeParam = Eigen::Matrix > > [ FAILED ] UnalignedMatrixTests/4.DefaultConstructorInitialization, where > > TypeParam = Eigen::Matrix > > [ FAILED ] UnalignedMatrixTests/5.DefaultConstructorInitialization, where > > TypeParam = Eigen::Matrix > > [ FAILED ] UnalignedVectorTests/4.DefaultConstructorInitialization, where > > TypeParam = Eigen::Matrix > > [ FAILED ] UnalignedVectorTests/6.DefaultConstructorInitialization, where > > TypeParam = Eigen::Matrix > > > > 7 FAILED TESTS > > > > 10/15 Test #2: SurgSimCollisionTest . Passed8.57 sec > > 11/15 Test #14: SurgSimParticlesTest . Passed 14.07 sec > > 12/15 Test #1: SurgSimBlocksTest Passed 15.19 sec > > 13/15 Test #11: SurgSimGraphicsTest .. Passed 20.38 sec > > 14/15 Test #10: SurgSimFrameworkTest . Passed 45.04 sec > > 15/15 Test #15: SurgSimPhysicsTest ... Passed 91.00 sec > > > > 93% tests passed, 1 tests failed out of 15 > > > > Total Test time (real) = 91.03 sec > > > > The following tests FAILED: > > 13 - SurgSimMathTest (Failed) > > Errors while running CTest > > Makefile:75: recipe for target 'test' failed > > make[2]: *** [test] Error 8 > > make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' > > dh_auto_test: make -j64 test ARGS+=-j64 returned exit code 2 > > debian/rules:39: recipe for target 'override_dh_auto_test' failed > > make[1]: *** [override_dh_auto_test] Error 2 > > make[1]: Leaving directory '/<>' > > debian/rules:7: recipe for target 'build' failed > > make: *** [build] Error 2 > > dpkg-buildpackage: error: debian/rules build gave error exit status 2 > > > > ___ > > Debian-med-packaging mailing list > > debian-med-packag...@lists.alioth.debian.org > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > > -- > http://fam-tille.de
Bug#831096: opensurgsim: FTBFS with GCC 6: cstdlib:75:25: fatal error: stdlib.h: No such file or directory
On Tue, Sep 6, 2016 at 4:06 PM, Andreas Tille wrote: [Paul, I wonder whether you realised the problems with opensurgsim] Thanks for the heads up. Graham's GCC6 patch works for me. I'll get it applied upstream. Hi Graham, On Thu, Aug 25, 2016 at 02:37:53PM +0200, Graham Inggs wrote: Hi Maintainer The attached patch fixes the FTBFS with GCC 6. I'll open a separate bug for the eigen3 issue and mark it as being blocked by #835411. I checked building opensurgsim and while I have not realised any problems directly hinting to eigen3 I've got: ... 2 FAILED TESTS Start 12: SurgSimPhysicsTest 12/12 Test #12: SurgSimPhysicsTest ... Passed0.64 sec 92% tests passed, 1 tests failed out of 12 Total Test time (real) = 8.99 sec The following tests FAILED: 11 - SurgSimMathTest (Failed) Errors while running CTest Makefile:130: recipe for target 'test' failed make[1]: *** [test] Error 8 make[1]: Leaving directory '/build/opensurgsim-0.6.0/obj-x86_64-linux-gnu' I am building now to see if I can reproduce this. SurgSimMathTest failure might be related to Eigen, but I'll let you know what I find. -Paul
Bug#803145: [Debian-med-packaging] Bug#803145: opensurgsim: FTBFS: static assertion failed: THIS_METHOD_IS_ONLY_FOR_INNER_OR_LAZY_PRODUCTS
On Tue, 2015-10-27 at 11:20 +, Chris Lamb wrote: > Source: opensurgsim > Version: 0.6.0-3 > Severity: serious > Justification: fails to build from source > User: reproducible-bui...@lists.alioth.debian.org > Usertags: ftbfs > X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org > > Dear Maintainer, > > opensurgsim fails to build from source in unstable/amd64. > > In file included from /usr/include/eigen3/Eigen/Core:297:0, > from > /build/opensurgsim- > 0.6.0/SurgSim/Math/Quaternion.h:24, > from > /build/opensurgsim- > 0.6.0/SurgSim/Collision/UnitTests/RepresentationUtilities.h:21, > from > /build/opensurgsim- > 0.6.0/SurgSim/Collision/UnitTests/ContactCalculationTestsCommon.h:22, > from > /build/opensurgsim- > 0.6.0/SurgSim/Collision/UnitTests/BoxPlaneContactCalculationTests.cpp > :16: > /usr/include/eigen3/Eigen/src/Core/Product.h: In instantiation of > 'Eigen::ProductImpl::Scalar > Eigen::ProductImpl::coeff(Eigen::Ind > ex, Eigen::Index) const [with Lhs = Eigen::Matrix; Rhs > = > Eigen::Matrix; int Option = 0; Eigen::ProductImpl Rhs, Option, Eigen::Dense>::Scalar = double; Eigen::In > dex = long int]': > /usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:749:31: require > d > from 'static void Eigen::internal::quaternionbase_assign_impl 3, > 3>::run(Eigen::QuaternionBase&, const > Other&) [with Derived = Eigen::Quaternion; Other = > Eigen::Product, Eigen::Matrix 3>, 0>]' > /usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:517:59: require > d > from 'Derived& Eigen::QuaternionBase::operator=(const > Eigen::MatrixBase&) [with OtherDerived = Eigen > ::Product, Eigen::Matrix, > 0>; > Derived = Eigen::Quaternion]' > /usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:267:72: require > d > from 'Eigen::Quaternion::Quaternion(const > Eigen::MatrixBase&) [with Derived = Eigen::Product > , Eigen::Matrix, 0>; > _Scalar = > double; int _Options = 0]' > /build/opensurgsim- > 0.6.0/SurgSim/Collision/UnitTests/BoxPlaneContactCalculationTests.cpp > :135:72: > required from here > /usr/include/eigen3/Eigen/src/Core/Product.h:203:7: error: static > assertion failed: THIS_METHOD_IS_ONLY_FOR_INNER_OR_LAZY_PRODUCTS > EIGEN_STATIC_ASSERT(EnableCoeff, > THIS_METHOD_IS_ONLY_FOR_INNER_OR_LAZY_PRODUCTS); > ^ > SurgSim/Collision/UnitTests/CMakeFiles/SurgSimCollisionTest.dir/build > .make:89: > recipe for target > 'SurgSim/Collision/UnitTests/CMakeFiles/SurgSimCollisionTest.dir/BoxD > oubleSidedPlaneContactCalcul > ationTests.cpp.o' failed > > [..] > > The full build log is attached or (an alternate build) can be viewed > here: > > https://reproducible.debian.net/logs/unstable/amd64/opensurgsim_0 > .6.0-3.build1.log.gz > Thanks for the bug report, I believe this is due to the recent Eigen update to 3.3-alpha1 in sid. I'll see what I can do. The likely solution is to upgrade OpenSurgSim to a new release, which should come out in a couple weeks. -Paul
Bug#798693: opensurgsim: FTBFS on i386 and powerpc: unaligned Eigen arrays
On Fri, 11 Sep 2015 14:44:15 -0400 "Aaron M. Ucko" wrote: > Source: opensurgsim > Version: 0.6.0-2 > Severity: serious > Justification: fails to build from source > > The i386 and powerpc builds of opensurgsim both failed because many > tests reported errors of the form > > SurgSim*Test: /usr/include/eigen3/Eigen/src/Core/DenseStorage.h:86: > Eigen::internal::plain_array 16>::plain_array() [with T = double; int Size = 16; int > MatrixOrArrayOptions = 0]: Assertion `(reinterpret_cast(eigen- > _unaligned_array_assert_workaround_gcc47(array)) & 0xf) == 0 && "this > assertion is explained here: " " > http://eigen.tuxfamily.org/dox-devel/group__TopicUnalignedArrayAssert.html"; > " READ THIS WEB PAGE !!! "' failed. > > (The powerpc build also encountered an unrelated test suite error, > which I'll report separately.) > > Could you please take a look? Per the error message, you may find > http://eigen.tuxfamily.org/dox-devel/group__TopicUnalignedArrayAssert.html > helpful. First off, thank you for organizing these build failures into bugs. This is great, and makes things much easier for me. There is a CMake variable to turn off eigen alignment in OpenSurgSim, and I have pushed a change that turns it off for i386 and powerpc to the package repository [1]. I also turned on some more unit tests that more aggressively test Eigen, to make sure we are ok on the other architectures. I'll push out a new version of OpenSurgSim soon with these changes. Thanks, -Paul [1] https://anonscm.debian.org/cgit/debian-med/opensurgsim.git/commit/?id=69a076e667dbf776369fba2876052f66282b2c7d
Bug#651433: patch to turn ITKVTKGLUE back on
Attached are 2 patches that will allow ITKVTKGLUE to be turned back on.
They make the ITKVTKGLUE module compatible with vtk 5.8. The first
patch, insighttoolkit.patch, actually needs to be applied to the
insighttoolkit source. The second patch, wrapitk.patch, is for the
wrapitk-python source.
diff --git a/debian/patches/itkvtkglue-vtk58.patch b/debian/patches/itkvtkglue-vtk58.patch
new file mode 100644
index 000..85b3750
--- /dev/null
+++ b/debian/patches/itkvtkglue-vtk58.patch
@@ -0,0 +1,29 @@
+--- a/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/Wrapping/itkvtk.swg
b/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/Wrapping/itkvtk.swg
+@@ -42,22 +42,22 @@
+
+ %typemap(out) vtkImageExport* {
+ PyImport_ImportModule("vtk");
+- $result = vtkPythonGetObjectFromPointer ( (vtkImageExport*)$1 );
++ $result = vtkPythonUtil::GetObjectFromPointer ( (vtkImageExport*)$1 );
+ }
+
+ %typemap(out) vtkImageImport* {
+ PyImport_ImportModule("vtk");
+- $result = vtkPythonGetObjectFromPointer ( (vtkImageImport*)$1 );
++ $result = vtkPythonUtil::GetObjectFromPointer ( (vtkImageImport*)$1 );
+ }
+
+ %typemap(out) vtkImageData* {
+ PyImport_ImportModule("vtk");
+- $result = vtkPythonGetObjectFromPointer ( (vtkImageData*)$1 );
++ $result = vtkPythonUtil::GetObjectFromPointer ( (vtkImageData*)$1 );
+ }
+
+ %typemap(in) vtkImageData* {
+ $1 = NULL;
+- $1 = (vtkImageData*) vtkPythonGetPointerFromObject ( $input, "vtkImageData" );
++ $1 = (vtkImageData*) vtkPythonUtil::GetPointerFromObject ( $input, "vtkImageData" );
+ if ( $1 == NULL ) { SWIG_fail; }
+ }
+
diff --git a/debian/patches/series b/debian/patches/series
index e895b96..1952557 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@ wrapitk.patch
wrapitk-externalprojects.patch
add-registration-optimizers.patch
wrap-iifilter-split.patch
+itkvtkglue-vtk58.patch
diff --git a/debian/rules b/debian/rules
index ec07f75..8ec30d5 100755
--- a/debian/rules
+++ b/debian/rules
@@ -37,8 +37,7 @@ CMAKE_FLAGS = \
-DWRAP_unsigned_short:BOOL=ON \
-DWRAP_vector_float:BOOL=ON \
-DWRAP_FFT:BOOL=OFF \
- -DWRAP_FFTW:BOOL=OFF \
- -DBUILD_ITKVTKGLUE:BOOL=OFF
+ -DWRAP_FFTW:BOOL=OFF
VER_FULL = $(VER_MAJOR).$(VER_MINOR).$(VER_PATCH)
SOVERSION = $(VER_MAJOR).$(VER_MINOR)
Bug#613539: insighttoolkit: FTBFS on multiple architectures
These are probably all caused by out of memory issues. Compiling this package with the new WrapITK python wrappings uses a lot of memory. It uses all my 8GB plus a little virtual memory on my machine (amd64). Although I use 3 cores. Increasing the memory (as Dominique showed above) or limiting the cores would probably solve this issue. Although I don't know how to do this. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
