[bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.

[Kei Kebreau]

Jonathan Brielmaier <address@hidden> writes:

> On 17/05/2018 13:39, Jonathan Brielmaier wrote:
>> On 17/05/2018 01:24, Kei Kebreau wrote:
>>>
>>> These patches are really just to upgrade Octave, but the old Shogun
>>> couldn't find the new version of Octave. The shogun update patch is a
>>> WIP, but I don't have enough RAM (only 3.8GB) to make it through Shogun's
>>> build process reliably. Could someone else help out with this patch?
>>>
>> 
>> I build shogun now, lets see how it goes :)
>
> Unfortunately there was a build error for shogun. I attached the build
> log where it fails. It has something to do with the eigen library...
>
>
>
> $ /pre-inst-env guix build shogun
> [...]
> [ 50%] Building CXX object 
> src/shogun/CMakeFiles/libshogun.dir/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp.o
> cd /tmp/guix-build-shogun-6.1.3.drv-0/build/src/shogun && 
> /gnu/store/cfdn69spjc44x4sd0acrwhxq6yay3rbc-gcc-5.5.0/bin/c++    
> -I/tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src 
> -I/tmp/guix-build-shogun-6.1.3.drv-0/build/src 
> -I/tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src/gpl -isystem 
> /gnu/store/iwzn3vhwmzkvhq7sqs6c4bjp2xld17kc-eigen-3.3.4/include/eigen3 
> -isystem /gnu/store/5s9am1dgn83wj5q5kwfcasqws8zd85zz-rxcpp-4.0.0 
> -I/gnu/store/mllyvfy39npzra984jsmcm8ksn3x8094-glpk-4.65/include 
> -I/gnu/store/wnw0gv5hgmhlw3jz1pgw4n017bhj9f2z-arpack-ng-3.5.0/lib/../include 
> -I/gnu/store/mv9m6bxdhijhlfvxpja3km6v599b4pv5-libxml2-2.9.7/include/libxml2 
> -I/gnu/store/27jrvwbg5xa9la6jwnqz6ys4k7pfyykl-hdf5-1.8.19/include 
> -I/gnu/store/9hd38bkw8bq8gq6lcv6vd8xjpcsbyzlm-zlib-1.2.11/include 
> -I/gnu/store/77l8sxh9py133cy1p9kypshji4q9wv0w-bzip2-1.0.6/include 
> -I/gnu/store/kgaf671a9a76k0ql1pwwjxjbj80x22mj-xz-5.2.3/include 
> -I/gnu/store/33m86ycak50vh2p0q7qb0byh990hrkjn-lzo-2.10/include  -Wall 
> -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow 
> -Wno-unknown-pragmas -Wno-deprecated  -O2 -g -DNDEBUG -fPIC   -fopenmp 
> -std=c++11 -o 
> CMakeFiles/libshogun.dir/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp.o
>  -c 
> /tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
> /tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp:15:45:
>  fatal error: unsupported/Eigen/MatrixFunctions: No such file or directory
> compilation terminated.
> make[2]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:11456: 
> src/shogun/CMakeFiles/libshogun.dir/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp.o]
>  Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[2]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build'
> make[1]: *** [CMakeFiles/Makefile2:126: 
> src/shogun/CMakeFiles/libshogun.dir/all] Error 2
> make[1]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build'
> make: *** [Makefile:153: all] Error 2
> phase `build' failed after 493.7 seconds
> builder for `/gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.drv' 
> failed with exit code 1
> @ build-failed /gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.drv - 
> 1 builder for `/gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.drv' 
> failed with exit code 1
> guix build: error: build failed: build of 
> `/gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.drv' failed

So it turns out that Eigen's source code comes with some functions that
are officially unsupported by the developers but still available for
use. Guix just doesn't install them. I've attached a patch that *should*
properly install the unsupported files to Eigen's include path.

Also, thanks for helping with this shogun patch!

0003-gnu-eigen-Install-unsupported-header-files.patch
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