[Bug 1223446] New: mono-shogun - Don't build with mono 4 - ml

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[Bug 1223446] New: mono-shogun - Don't build with mono 4

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Red Hat Bugzilla

20 May 2015 20 May '15

9:11 a.m.

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

Bug ID: 1223446 Summary: mono-shogun - Don't build with mono 4 Product: Fedora Version: rawhide Component: shogun Assignee: bjoern.esser@gmail.com Reporter: claudiorodrigo@pereyradiaz.com.ar QA Contact: extras-qa@fedoraproject.org CC: bjoern.esser@gmail.com, lupinix@mailbox.org, ml@lists.fedoraproject.org

Require fix spec and maybe patches to build with mono 4x Need move to profile 4.5

See: https://fedoraproject.org/wiki/Changes/Mono_4

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Red Hat Bugzilla

20 May 20 May

9:11 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

Claudio Rodrigo Pereyra DIaz claudiorodrigo@pereyradiaz.com.ar changed:

What |Removed |Added ---------------------------------------------------------------------------- Blocks| |1221559

Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1221559 [Bug 1221559] Mono 4

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Red Hat Bugzilla

21 May 21 May

1:49 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

Timotheus Pokorra timotheus.pokorra@solidcharity.com changed:

--- Comment #1 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- currently, the build on Koji for Rawhide fails much earlier, before Mono is involved: http://koji.fedoraproject.org/koji/packageinfo?packageID=17486

I did a build on F21 with mono4 installed, which took much longer. I got trouble with generated code in /root/rpmbuild/BUILD/shogun-4.0.0/build-x86-64.fc21/src/interfaces/csharp_modular/modshogunPINVOKE.cs

/usr/bin/mcs /t:library *.cs /out:modshogun.dll modshogunPINVOKE.cs(7271,137): error CS0100: The parameter name `size' is a duplicate modshogunPINVOKE.cs(17102,255+): error CS0100: The parameter name `size' is a duplicate modshogunPINVOKE.cs(17888,190): error CS0100: The parameter name `size' is a duplicate modshogunPINVOKE.cs(17891,190): error CS0100: The parameter name `size' is a duplicate modshogunPINVOKE.cs(19190,192): error CS0100: The parameter name `size' is a duplicate

and many more errors like this.

The code for example in line 7271 looks like this: public static extern global::System.IntPtr new_IndexBlockTree__SWIG_3(int size, [MarshalAs(UnmanagedType.LPArray)]double[] jarg1, int size, [MarshalAs(UnmanagedType.LPArray)]double[] jarg2);

hope this helps...

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Red Hat Bugzilla

17 Jun 17 Jun

1:07 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #2 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- Thanks Björn, Rawhide does now get to the "The parameter name `size' is a duplicate" error!

https://github.com/shogun-toolbox/shogun/issues/2425 looks like a similar bug, but did not receive any attention upstream: modshogunPINVOKE.cs(9270,141): error CS0100: The parameter name `rows' is a duplicate

Can you please follow the "duplicate parameter size" problem up with upstream?

Thanks!

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Red Hat Bugzilla

23 Jun 23 Jun

4:50 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #3 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- Updated https://github.com/shogun-toolbox/shogun/issues/2425

One solution would be to ignore those methods, but then we would lose them.

This is a problem of SWIG creating invalid code.

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Red Hat Bugzilla

4:52 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #4 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- Created attachment 1042196 --> https://bugzilla.redhat.com/attachment.cgi?id=1042196&action=edit some log of the errors. including the commands to build it

this log might help to reproduce the error without having to wait for the full rebuild...

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Red Hat Bugzilla

4:56 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #5 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- Created attachment 1042198 --> https://bugzilla.redhat.com/attachment.cgi?id=1042198&action=edit the file that has the broken code

this might help to see which methods are affected

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Red Hat Bugzilla

24 Jun 24 Jun

11:38 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #6 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- I have reported this issue at the swig project: https://github.com/swig/swig/issues/448

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Red Hat Bugzilla

25 Jun 25 Jun

2:06 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #7 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- Got a reply from the swig project. It seems that the use of the inattributes by shogun is not correct.

Please see my comment: https://github.com/shogun-toolbox/shogun/issues/2425#issuecomment-115132055

Probably best would be to work on a test case similar to the test cases provided by Swig.

But I guess this becomes more of a task for a developer rather than a packager, so I think I need to pull out now... I still have not figured out (did not look for it) what the purpose of shogun is, so I leave this to people more interested in it :)

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Red Hat Bugzilla

6 Aug 6 Aug

3:32 p.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #9 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- Created attachment 1060073 --> https://bugzilla.redhat.com/attachment.cgi?id=1060073&action=edit patch to ignore methods and classes for src/interfaces/csharp_modular/modshogunPINVOKE.cs to compile

I have uploaded the patch that will ignore some of the methods that create invalid C# code. Now src/interfaces/csharp_modular/modshogunPINVOKE.cs can be compiled.

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Red Hat Bugzilla

7 Aug 7 Aug

2:06 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #10 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- unfortunately, the c# examples don't build anymore after ignoring these methods and classes when I built with rpmbuild -ba SPECS/shogun.spec --without java --without lua --without octave --without r --without ruby --without python --without python3 --without cli --without memtest --without testsuite

Also when I build on Koji, I get errors in the java examples, even though I have an ifdef for CSharp only for ignoring those methods and classes: https://koji.fedoraproject.org/koji/taskinfo?taskID=10626687 [ 88%] Generating kernel_histogram_word_string_modular.class cd /builddir/build/BUILD/shogun-4.0.0/build-x86-64.fc24/examples/undocumented/java_modular && /usr/bin/javac -cp /usr/lib/java/jblas.jar:/builddir/build/BUILD/shogun-4.0.0/build-x86-64.fc24/src/interfaces/java_modular/shogun.jar:/builddir/build/BUILD/shogun-4.0.0/build-x86-64.fc24/examples/undocumented/java_modular -d /builddir/build/BUILD/shogun-4.0.0/build-x86-64.fc24/examples/undocumented/java_modular /builddir/build/BUILD/shogun-4.0.0/examples/undocumented/java_modular/kernel_histogram_word_string_modular.java /builddir/build/BUILD/shogun-4.0.0/examples/undocumented/java_modular/preprocessor_sortulongstring_modular.java:37: error: cannot find symbol CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, false); ^ symbol: class CommUlongStringKernel location: class preprocessor_sortulongstring_modular /builddir/build/BUILD/shogun-4.0.0/examples/undocumented/java_modular/preprocessor_sortulongstring_modular.java:37: error: cannot find symbol CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, false); ^ symbol: class CommUlongStringKernel location: class preprocessor_sortulongstring_modular 2 errors examples/undocumented/java_modular/CMakeFiles/build_java_examples.dir/build.make:453: recipe for target 'examples/undocumented/java_modular/preprocessor_sortulongstring_modular.class' failed make[2]: *** [examples/undocumented/java_modular/preprocessor_sortulongstring_modular.class] Error 1 make[2]: *** Waiting for unfinished jobs.... /builddir/build/BUILD/shogun-4.0.0/examples/undocumented/java_modular/kernel_comm_ulong_string_modular.java:36: error: cannot find symbol CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, use_sign); ^ symbol: class CommUlongStringKernel location: class kernel_comm_ulong_string_modular /builddir/build/BUILD/shogun-4.0.0/examples/undocumented/java_modular/kernel_comm_ulong_string_modular.java:36: error: cannot find symbol CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, use_sign); ^ symbol: class CommUlongStringKernel location: class kernel_comm_ulong_string_modular 2 errors

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Red Hat Bugzilla

2:12 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #11 from Timotheus Pokorra timotheus.pokorra@solidcharity.com --- I think the support for C# needs to be resolved upstream, in the shogun project, as it was discussed on IRC fedora-de.

I tried to build shogun without mono (replacing "with mono" with "with monoOff" in the spec file), but now I get errors already here: https://kojipkgs.fedoraproject.org//work/tasks/2514/10632514/build.log [ 52%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/base/class_list.cpp.o cd /builddir/build/BUILD/shogun-4.0.0/build-x86-32.fc24/src/shogun && /usr/bin/c++ -DDSFMT_MEXP=19937 -DHAVE_ARPACK -DHAVE_ARPREC -DHAVE_ATLAS -DHAVE_COLPACK -DHAVE_CURL -DHAVE_CXX11 -DHAVE_CXX11_ATOMIC -DHAVE_DECL_ISINF -DHAVE_DECL_ISNAN -DHAVE_DECL_SIGNGAM -DHAVE_DOXYGEN -DHAVE_EIGEN3 -DHAVE_FPCLASS -DHAVE_HDF5 -DHAVE_ISINF -DHAVE_ISNAN -DHAVE_JBLAS -DHAVE_JSON -DHAVE_LAPACK -DHAVE_LARGEFILE -DHAVE_LGAMMAL -DHAVE_LINALG_LIB -DHAVE_LOG2 -DHAVE_NLOPT -DHAVE_OCTAVE -DHAVE_POWL -DHAVE_PROTOBUF -DHAVE_PTHREAD -DHAVE_PYTHON -DHAVE_SQRTL -DHAVE_STD_ISFINITE -DHAVE_STD_ISINF -DHAVE_STD_ISNAN -DHAVE_STD_UNORDERED_MAP -DHAVE_XML -DINVERSE_ACTIVE=INVERSE_LUSOL -DOCTAVE_APIVERSION=50 -DPARSER_LP -DRoleIsExternalInvEngine -DSFMT_MEXP=19937 -DSHOGUN -DSWIG_TYPE_TABLE=shogun -DUSE_BIGSTATES -DUSE_BOOL -DUSE_BZIP2 -DUSE_CHAR -DUSE_COMPLEX128 -DUSE_FLOAT32 -DUSE_FLOAT64 -DUSE_GLPK -DUSE_GZIP -DUSE_HMMCACHE -DUSE_INT32 -DUSE_INT64 -DUSE_LPSOLVE -DUSE_LZMA -DUSE_LZO -DUSE_REFERENCE_COUNTING -DUSE_SHORTREAL_KERNELCACHE -DUSE_SNAPPY -DUSE_SPINLOCKS -DUSE_UINT16 -DUSE_UINT64 -DUSE_UINT8 -DYY_NEVER_INTERACTIVE -std=c++11 -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -fopenmp -O2 -O2 -g -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fPIC -I/builddir/build/BUILD/shogun-4.0.0/src -I/builddir/build/BUILD/shogun-4.0.0/src/shogun -I/builddir/build/BUILD/shogun-4.0.0/build-x86-32.fc24/src -I/builddir/build/BUILD/shogun-4.0.0/build-x86-32.fc24/src/shogun -isystem /usr/include/eigen3 -I/usr/lib/../include -I/usr/include/json-c -I/usr/include/libxml2 -o CMakeFiles/libshogun.dir/base/class_list.cpp.o -c /builddir/build/BUILD/shogun-4.0.0/src/shogun/base/class_list.cpp In file included from /builddir/build/BUILD/shogun-4.0.0/src/shogun/kernel/normalizer/KernelNormalizer.h:16:0, from /builddir/build/BUILD/shogun-4.0.0/src/shogun/transfer/multitask/MultitaskKernelMaskNormalizer.h:16, from /builddir/build/BUILD/shogun-4.0.0/src/shogun/base/class_list.cpp:16: /builddir/build/BUILD/shogun-4.0.0/src/shogun/kernel/Kernel.h: In member function 'float64_t shogun::CKernel::kernel(int32_t, int32_t)': /builddir/build/BUILD/shogun-4.0.0/src/shogun/kernel/Kernel.h:207:21: error: invalid use of incomplete type 'class shogun::CKernelNormalizer' return normalizer->normalize(compute(idx_a, idx_b), idx_a, idx_b); ^ In file included from /builddir/build/BUILD/shogun-4.0.0/src/shogun/kernel/normalizer/KernelNormalizer.h:16:0, from /builddir/build/BUILD/shogun-4.0.0/src/shogun/transfer/multitask/MultitaskKernelMaskNormalizer.h:16, from /builddir/build/BUILD/shogun-4.0.0/src/shogun/base/class_list.cpp:16: /builddir/build/BUILD/shogun-4.0.0/src/shogun/kernel/Kernel.h:32:8: note: forward declaration of 'class shogun::CKernelNormalizer' class CKernelNormalizer; ^ src/shogun/CMakeFiles/libshogun.dir/build.make:16432: recipe for target 'src/shogun/CMakeFiles/libshogun.dir/base/class_list.cpp.o' failed

I give up again, I hope someone can make sense of it...

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Red Hat Bugzilla

14 Sep 14 Sep

8:21 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

Claudio Rodrigo Pereyra DIaz claudiorodrigo@pereyradiaz.com.ar changed:

What |Removed |Added ---------------------------------------------------------------------------- Blocks|1221559 |

--- Comment #12 from Claudio Rodrigo Pereyra DIaz claudiorodrigo@pereyradiaz.com.ar --- 4.0.0-6 - temporarily disabling Mono-bindings on Fedora 23+

No longer block Mono 4 Change

Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1221559 [Bug 1221559] Mono 4

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Red Hat Bugzilla

26 Jan 26 Jan

10:10 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #13 from Fedora Update System updates@fedoraproject.org --- arprec-2.2.18-1.fc23 shogun-4.0.1-0.9.git20160125.0382808.fc23 has been submitted as an update to Fedora 23. https://bodhi.fedoraproject.org/updates/FEDORA-2016-600a58722b

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Red Hat Bugzilla

10:10 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

Fedora Update System updates@fedoraproject.org changed:

What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |MODIFIED

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Red Hat Bugzilla

28 Jan 28 Jan

4:27 p.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

Fedora Update System updates@fedoraproject.org changed:

What |Removed |Added ---------------------------------------------------------------------------- Status|MODIFIED |ON_QA

--- Comment #14 from Fedora Update System updates@fedoraproject.org --- arprec-2.2.18-1.fc23, shogun-4.0.1-0.9.git20160125.0382808.fc23 has been pushed to the Fedora 23 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2016-600a58722b

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Red Hat Bugzilla

10 Feb 10 Feb

10:52 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

--- Comment #15 from Fedora Update System updates@fedoraproject.org --- arprec-2.2.18-1.fc23, shogun-4.0.1-0.9.git20160125.0382808.fc23 has been pushed to the Fedora 23 stable repository. If problems still persist, please make note of it in this bug report.

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Red Hat Bugzilla

10:52 a.m.

New subject: [Bug 1223446] mono-shogun - Don't build with mono 4

https://bugzilla.redhat.com/show_bug.cgi?id=1223446

Fedora Update System updates@fedoraproject.org changed:

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