[PATCH 1/3] gnu: octave: Update to 4.4.0.

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4 participants
  • Jonathan Brielmaier
  • Kei Kebreau
  • Ludovic Courtès
  • Ricardo Wurmus
Owner
unassigned
Submitted by
Kei Kebreau
Severity
normal
K
K
Kei Kebreau wrote on 17 May 2018 01:10
(address . guix-patches@gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)
20180516231033.1680-1-kkebreau@posteo.net
* gnu/packages/maths.scm (octave): Update to 4.4.0.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2e6f79ad5..e9a6ceaab 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1323,7 +1323,7 @@ can solve two kinds of problems:
(define-public octave
(package
(name "octave")
- (version "4.2.2")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
@@ -1331,7 +1331,7 @@ can solve two kinds of problems:
version ".tar.lz"))
(sha256
(base32
- "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp"))))
+ "0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
--
2.17.0
K
K
Kei Kebreau wrote on 17 May 2018 01:19
[PATCH 2/3] gnu: Add rxcpp.
(address . 31479@debbugs.gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)
20180516231957.1827-1-kkebreau@posteo.net
* gnu/packages/machine-learning.scm (rxcpp): New variable.
---
gnu/packages/machine-learning.scm | 42 +++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)

Toggle diff (62 lines)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index f0d35484e..6536d861e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
@@ -501,6 +502,47 @@ tools. This enables both rapid prototyping of data pipelines and extensibility
in terms of new algorithms.")
(license license:gpl3+)))
+(define-public rxcpp
+ (package
+ (name "rxcpp")
+ (version "4.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
+ (file-name (string-append name "-" version ".tar.gz"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'remove-werror
+ (lambda _
+ (substitute* (find-files ".")
+ (("-Werror") ""))
+ #t))
+ (replace 'check
+ (lambda _
+ (invoke "ctest"))))))
+ (native-inputs
+ `(("catch" ,catch-framework)))
+ (home-page "http://reactivex.io/")
+ (synopsis "Reactive Extensions for C++")
+ (description
+ "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
+values-distributed-in-time. ReactiveX is a library for composing asynchronous
+and event-based programs by using observable sequences.
+
+It extends the observer pattern to support sequences of data and/or events and
+adds operators that allow you to compose sequences together declaratively while
+abstracting away concerns about things like low-level threading,
+synchronization, thread-safety, concurrent data structures, and non-blocking
+I/O.")
+ (license license:asl2.0)))
+
(define-public r-adaptivesparsity
(package
(name "r-adaptivesparsity")
--
2.17.0
K
K
Kei Kebreau wrote on 17 May 2018 01:19
[PATCH 3/3] gnu: Update shogun to 6.1.3.
(address . 31479@debbugs.gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)
20180516231957.1827-2-kkebreau@posteo.net
* gnu/packages/machine-learning.scm (shogun): Update to 6.1.3.
[arguments]: Rewrite list of symlinks in 'delete-broken-symlinks' phase.
Rewrite file lists given to substitute* in 'change-R-target-path' and
'fix-octave-modules' phases. Add 'move-rxcpp' phase. Rewrite configure-flags
for the update.
[inputs]: Add eigen.
[native-inputs]: Add rxcpp.
---
gnu/packages/machine-learning.scm | 60 ++++++++++++++-----------------
1 file changed, 27 insertions(+), 33 deletions(-)

Toggle diff (127 lines)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 6536d861e..e79aa6692 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -37,6 +37,7 @@
#:use-module (guix build-system r)
#:use-module (guix git-download)
#:use-module (gnu packages)
+ #:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
@@ -367,7 +368,7 @@ sample proximities between pairs of cases.")
(define-public shogun
(package
(name "shogun")
- (version "4.0.0")
+ (version "6.1.3")
(source
(origin
(method url-fetch)
@@ -377,7 +378,7 @@ sample proximities between pairs of cases.")
"/sources/shogun-" version ".tar.bz2"))
(sha256
(base32
- "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
+ "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
(modules '((guix build utils)
(ice-9 rdelim)))
(snippet
@@ -423,62 +424,54 @@ sample proximities between pairs of cases.")
"applications/easysvm/data"
"applications/msplicer/data"
"applications/ocr/data"
- "examples/documented/data"
- "examples/documented/matlab_static"
- "examples/documented/octave_static"
- "examples/undocumented/data"
- "examples/undocumented/matlab_static"
- "examples/undocumented/octave_static"
- "tests/integration/data"
- "tests/integration/matlab_static"
- "tests/integration/octave_static"
- "tests/integration/python_modular/tests"))
+ "examples/meta/data"
+ "examples/undocumented/data"))
#t))
(add-after 'unpack 'change-R-target-path
(lambda* (#:key outputs #:allow-other-keys)
- (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
- "src/interfaces/r_static/CMakeLists.txt"
- "examples/undocumented/r_modular/CMakeLists.txt")
+ (substitute* '("src/interfaces/r/CMakeLists.txt"
+ "examples/meta/r/CMakeLists.txt")
(("\\$\\{R_COMPONENT_LIB_PATH\\}")
(string-append (assoc-ref outputs "out")
"/lib/R/library/")))
#t))
(add-after 'unpack 'fix-octave-modules
(lambda* (#:key outputs #:allow-other-keys)
- (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
- "src/interfaces/octave_static/CMakeLists.txt")
+ (substitute* "src/interfaces/octave/CMakeLists.txt"
(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
- "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
-
- ;; change target directory
- (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
+ "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
+ ;; change target directory
(("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
(string-append (assoc-ref outputs "out")
"/share/octave/packages")))
#t))
+ (add-after 'unpack 'move-rxcpp
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((rxcpp-dir "shogun/third-party/rxcpp"))
+ (mkdir-p rxcpp-dir)
+ (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
+ #t)))
(add-before 'build 'set-HOME
;; $HOME needs to be set at some point during the build phase
(lambda _ (setenv "HOME" "/tmp") #t)))
#:configure-flags
(list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
"-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
- ;;"-DJavaModular=ON" ;requires unpackaged jblas
- ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
- ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
- ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file
- "-DOctaveModular=ON"
- "-DOctaveStatic=ON"
- "-DPythonModular=ON"
- "-DPythonStatic=ON"
- "-DRModular=ON"
- "-DRStatic=ON"
- "-DCmdLineStatic=ON")))
+ "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
+ ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
+ ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
+ ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
+ ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
+ "-DINTERFACE_OCTAVE=ON"
+ "-DINTERFACE_PYTHON=ON"
+ "-DINTERFACE_R=ON")))
(inputs
`(("python" ,python)
("numpy" ,python-numpy)
("r-minimal" ,r-minimal)
("octave" ,octave)
("swig" ,swig)
+ ("eigen" ,eigen)
("hdf5" ,hdf5)
("atlas" ,atlas)
("arpack" ,arpack-ng)
@@ -488,7 +481,8 @@ sample proximities between pairs of cases.")
("lzo" ,lzo)
("zlib" ,zlib)))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ `(("pkg-config" ,pkg-config)
+ ("rxcpp" ,rxcpp)))
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(supported-systems '("x86_64-linux"))
--
2.17.0
K
K
Kei Kebreau wrote on 17 May 2018 01:24
(address . 31479@debbugs.gnu.org)
874lj7w5f2.fsf@posteo.net
Kei Kebreau <kkebreau@posteo.net> writes:

Toggle quote (137 lines)
> * gnu/packages/machine-learning.scm (shogun): Update to 6.1.3.
> [arguments]: Rewrite list of symlinks in 'delete-broken-symlinks' phase.
> Rewrite file lists given to substitute* in 'change-R-target-path' and
> 'fix-octave-modules' phases. Add 'move-rxcpp' phase. Rewrite configure-flags
> for the update.
> [inputs]: Add eigen.
> [native-inputs]: Add rxcpp.
> ---
> gnu/packages/machine-learning.scm | 60 ++++++++++++++-----------------
> 1 file changed, 27 insertions(+), 33 deletions(-)
>
> diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
> index 6536d861e..e79aa6692 100644
> --- a/gnu/packages/machine-learning.scm
> +++ b/gnu/packages/machine-learning.scm
> @@ -37,6 +37,7 @@
> #:use-module (guix build-system r)
> #:use-module (guix git-download)
> #:use-module (gnu packages)
> + #:use-module (gnu packages algebra)
> #:use-module (gnu packages autotools)
> #:use-module (gnu packages boost)
> #:use-module (gnu packages check)
> @@ -367,7 +368,7 @@ sample proximities between pairs of cases.")
> (define-public shogun
> (package
> (name "shogun")
> - (version "4.0.0")
> + (version "6.1.3")
> (source
> (origin
> (method url-fetch)
> @@ -377,7 +378,7 @@ sample proximities between pairs of cases.")
> "/sources/shogun-" version ".tar.bz2"))
> (sha256
> (base32
> - "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
> + "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
> (modules '((guix build utils)
> (ice-9 rdelim)))
> (snippet
> @@ -423,62 +424,54 @@ sample proximities between pairs of cases.")
> "applications/easysvm/data"
> "applications/msplicer/data"
> "applications/ocr/data"
> - "examples/documented/data"
> - "examples/documented/matlab_static"
> - "examples/documented/octave_static"
> - "examples/undocumented/data"
> - "examples/undocumented/matlab_static"
> - "examples/undocumented/octave_static"
> - "tests/integration/data"
> - "tests/integration/matlab_static"
> - "tests/integration/octave_static"
> - "tests/integration/python_modular/tests"))
> + "examples/meta/data"
> + "examples/undocumented/data"))
> #t))
> (add-after 'unpack 'change-R-target-path
> (lambda* (#:key outputs #:allow-other-keys)
> - (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
> - "src/interfaces/r_static/CMakeLists.txt"
> - "examples/undocumented/r_modular/CMakeLists.txt")
> + (substitute* '("src/interfaces/r/CMakeLists.txt"
> + "examples/meta/r/CMakeLists.txt")
> (("\\$\\{R_COMPONENT_LIB_PATH\\}")
> (string-append (assoc-ref outputs "out")
> "/lib/R/library/")))
> #t))
> (add-after 'unpack 'fix-octave-modules
> (lambda* (#:key outputs #:allow-other-keys)
> - (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
> - "src/interfaces/octave_static/CMakeLists.txt")
> + (substitute* "src/interfaces/octave/CMakeLists.txt"
> (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
> - "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
> -
> - ;; change target directory
> - (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
> + "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
> + ;; change target directory
> (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
> (string-append (assoc-ref outputs "out")
> "/share/octave/packages")))
> #t))
> + (add-after 'unpack 'move-rxcpp
> + (lambda* (#:key inputs #:allow-other-keys)
> + (let ((rxcpp-dir "shogun/third-party/rxcpp"))
> + (mkdir-p rxcpp-dir)
> + (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
> + #t)))
> (add-before 'build 'set-HOME
> ;; $HOME needs to be set at some point during the build phase
> (lambda _ (setenv "HOME" "/tmp") #t)))
> #:configure-flags
> (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
> "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
> - ;;"-DJavaModular=ON" ;requires unpackaged jblas
> - ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
> - ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
> - ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file
> - "-DOctaveModular=ON"
> - "-DOctaveStatic=ON"
> - "-DPythonModular=ON"
> - "-DPythonStatic=ON"
> - "-DRModular=ON"
> - "-DRStatic=ON"
> - "-DCmdLineStatic=ON")))
> + "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
> + ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
> + ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
> + ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
> + ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
> + "-DINTERFACE_OCTAVE=ON"
> + "-DINTERFACE_PYTHON=ON"
> + "-DINTERFACE_R=ON")))
> (inputs
> `(("python" ,python)
> ("numpy" ,python-numpy)
> ("r-minimal" ,r-minimal)
> ("octave" ,octave)
> ("swig" ,swig)
> + ("eigen" ,eigen)
> ("hdf5" ,hdf5)
> ("atlas" ,atlas)
> ("arpack" ,arpack-ng)
> @@ -488,7 +481,8 @@ sample proximities between pairs of cases.")
> ("lzo" ,lzo)
> ("zlib" ,zlib)))
> (native-inputs
> - `(("pkg-config" ,pkg-config)))
> + `(("pkg-config" ,pkg-config)
> + ("rxcpp" ,rxcpp)))
> ;; Non-portable SSE instructions are used so building fails on platforms
> ;; other than x86_64.
> (supported-systems '("x86_64-linux"))

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?
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L
L
Ludovic Courtès wrote on 17 May 2018 13:24
Re: [bug#31479] [PATCH 1/3] gnu: octave: Update to 4.4.0.
(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 31479@debbugs.gnu.org)
87h8n634pk.fsf@gnu.org
Kei Kebreau <kkebreau@posteo.net> skribis:

Toggle quote (2 lines)
> * gnu/packages/maths.scm (octave): Update to 4.4.0.

LGTM, thanks!

Ludo'.
L
L
Ludovic Courtès wrote on 17 May 2018 13:26
Re: [bug#31479] [PATCH 2/3] gnu: Add rxcpp.
(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 31479@debbugs.gnu.org)
87d0xu34mu.fsf@gnu.org
Kei Kebreau <kkebreau@posteo.net> skribis:

Toggle quote (2 lines)
> * gnu/packages/machine-learning.scm (rxcpp): New variable.

[...]

Toggle quote (7 lines)
> + (home-page "http://reactivex.io/")
> + (synopsis "Reactive Extensions for C++")
> + (description
> + "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
> +values-distributed-in-time. ReactiveX is a library for composing asynchronous
> +and event-based programs by using observable sequences.

LGTM!

Probably machine-learning.scm is not the best place for it, but I can’t
think of a better place.

Thanks,
Ludo’.
J
J
Jonathan Brielmaier wrote on 17 May 2018 13:39
Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
(address . guix-patches@gnu.org)
0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de
On 17/05/2018 01:24, Kei Kebreau wrote:
Toggle quote (7 lines)
>
> 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 :)
J
J
Jonathan Brielmaier wrote on 18 May 2018 07:58
(address . guix-patches@gnu.org)
0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de
On 17/05/2018 13:39, Jonathan Brielmaier wrote:
Toggle quote (10 lines)
> 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
K
K
Kei Kebreau wrote on 18 May 2018 19:08
(name . Jonathan Brielmaier)(address . jonathan.brielmaier@web.de)(address . 31479@debbugs.gnu.org)
87muww6gd2.fsf@posteo.net
Jonathan Brielmaier <jonathan.brielmaier@web.de> writes:

Toggle quote (33 lines)
> 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!
From eed3dcce3714bc16ccb378d261d9e1bd8db3c249 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Fri, 18 May 2018 12:46:57 -0400
Subject: [PATCH 3/4] gnu: eigen: Install unsupported header files.

* gnu/packages/algebra.scm (eigen)[arguments]: Add 'install-unsupported' phase.
Use invoke instead of system*.
---
gnu/packages/algebra.scm | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)

Toggle diff (35 lines)
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 03a61be47..51be58ee2 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -750,6 +750,14 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
#:build-type "Release"
#:phases (modify-phases %standard-phases
+ (add-after 'install 'install-unsupported
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (include (string-append out "/include/eigen3")))
+ (copy-recursively "unsupported"
+ (string-append include
+ "/unsupported"))
+ #t)))
(replace 'check
(lambda _
(let* ((cores (parallel-job-count))
@@ -757,11 +765,11 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
(setenv "EIGEN_SEED" "1") ;for reproducibility
;; First build the tests, in parallel. See
;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
- (and (zero? (system* "make" "buildtests" dash-j))
+ (and (invoke "make" "buildtests" dash-j)
;; Then run 'CTest' with -V so we get more
;; details upon failure.
- (zero? (system* "ctest" "-V" dash-j)))))))))
+ (invoke "ctest" "-V" dash-j))))))))
(home-page "http://eigen.tuxfamily.org")
(synopsis "C++ template library for linear algebra")
(description
--
2.17.0
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L
L
Ludovic Courtès wrote on 19 May 2018 22:18
(name . Kei Kebreau)(address . kkebreau@posteo.net)
87fu2npfgl.fsf@gnu.org
Hello,

Kei Kebreau <kkebreau@posteo.net> skribis:

Toggle quote (5 lines)
> 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.

Ricardo has a similar patch in the Tensorflow series:


Could the two of you see how the two patches should be merged? :-)

Thanks,
Ludo’.
K
K
Kei Kebreau wrote on 20 May 2018 20:31
(name . Ludovic Courtès)(address . ludo@gnu.org)
87h8n25gbv.fsf@posteo.net
ludo@gnu.org (Ludovic Courtès) writes:

Toggle quote (18 lines)
> Hello,
>
> Kei Kebreau <kkebreau@posteo.net> skribis:
>
>> 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.
>
> Ricardo has a similar patch in the Tensorflow series:
>
> https://bugs.gnu.org/31386
>
> Could the two of you see how the two patches should be merged? :-)
>
> Thanks,
> Ludo’.

Hi,

Thanks for the heads up! Looking at Ricardo's patch, it looks like the
same goal is accomplished in a cleaner fashion. I'll test it today and
report back results. I've been working on shogun during the past few
days and it may soon be finished.
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R
R
Ricardo Wurmus wrote on 24 May 2018 11:09
(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 31479@debbugs.gnu.org)
87a7spcte2.fsf@mdc-berlin.de
Hi Kei,

please also note that Shogun contains references to proprietary
software. It has support for SVMLight, which is non-free software. It
includes a script to remove all references to and adapters for SVMLight,
but unfortunately we cannot run shell scripts in a snippet. Changing
this requires changing the “package” syntax to delay evaluation more.

Until then we need to remove the non-free bits in code, which is what
the current snippet does, but the code would need to be adjusted for
version 6.1.3.

Thanks for taking this on!

--
Ricardo
K
K
Kei Kebreau wrote on 27 May 2018 03:21
(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
87po1hnba0.fsf@posteo.net
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

Toggle quote (17 lines)
> Hi Kei,
>
> please also note that Shogun contains references to proprietary
> software. It has support for SVMLight, which is non-free software. It
> includes a script to remove all references to and adapters for SVMLight,
> but unfortunately we cannot run shell scripts in a snippet. Changing
> this requires changing the “package” syntax to delay evaluation more.
>
> Until then we need to remove the non-free bits in code, which is what
> the current snippet does, but the code would need to be adjusted for
> version 6.1.3.
>
> Thanks for taking this on!
>
> --
> Ricardo

Thank you for the tip!

I've attached the four patches that make it possible to build Shogun
6.1.3 successfully, and I'm just looking through the source code to
remove the proprietary bits.

P.S. Ricardo, you'll notice the eigen patch is actually yours from
another patchset! I verified that it works as expected.
From 0243faa33cc2c33ed7160ab754ad45ceff626eb2 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sat, 5 May 2018 10:21:38 -0400
Subject: [PATCH 1/5] gnu: octave: Update to 4.4.0.

* gnu/packages/maths.scm (octave): Update to 4.4.0.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a36d2333e..97f847665 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1332,7 +1332,7 @@ can solve two kinds of problems:
(define-public octave
(package
(name "octave")
- (version "4.2.2")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
@@ -1340,7 +1340,7 @@ can solve two kinds of problems:
version ".tar.lz"))
(sha256
(base32
- "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp"))))
+ "0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
--
2.17.0
From 50b6630e06f434237c1014765444d01a38f40e61 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Wed, 9 May 2018 10:01:40 -0400
Subject: [PATCH 2/5] gnu: Add rxcpp.

* gnu/packages/machine-learning.scm (rxcpp): New variable.
---
gnu/packages/machine-learning.scm | 42 +++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)

Toggle diff (62 lines)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index f0d35484e..6536d861e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
@@ -501,6 +502,47 @@ tools. This enables both rapid prototyping of data pipelines and extensibility
in terms of new algorithms.")
(license license:gpl3+)))
+(define-public rxcpp
+ (package
+ (name "rxcpp")
+ (version "4.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
+ (file-name (string-append name "-" version ".tar.gz"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'remove-werror
+ (lambda _
+ (substitute* (find-files ".")
+ (("-Werror") ""))
+ #t))
+ (replace 'check
+ (lambda _
+ (invoke "ctest"))))))
+ (native-inputs
+ `(("catch" ,catch-framework)))
+ (home-page "http://reactivex.io/")
+ (synopsis "Reactive Extensions for C++")
+ (description
+ "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
+values-distributed-in-time. ReactiveX is a library for composing asynchronous
+and event-based programs by using observable sequences.
+
+It extends the observer pattern to support sequences of data and/or events and
+adds operators that allow you to compose sequences together declaratively while
+abstracting away concerns about things like low-level threading,
+synchronization, thread-safety, concurrent data structures, and non-blocking
+I/O.")
+ (license license:asl2.0)))
+
(define-public r-adaptivesparsity
(package
(name "r-adaptivesparsity")
--
2.17.0
From 593edb81de8b6ad064d388aa39896ef8667e06bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus at>
Date: Tue, 8 May 2018 16:59:07 +0200
Subject: [PATCH 3/5] gnu: eigen: Include unsupported features.

* gnu/packages/algebra.scm (eigen)[source]: Do not build the tests for
unsupported features, but include the files.

Signed-off-by: Kei Kebreau <kkebreau@posteo.net>
---
gnu/packages/algebra.scm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)

Toggle diff (19 lines)
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 210b734b9..ff8478c50 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -732,9 +732,10 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
;; but maintainers say it's a known issue and it's unsupported
;; anyway, so just skip them.
'(begin
+ (substitute* "unsupported/CMakeLists.txt"
+ (("add_subdirectory\\(test.*")
+ "# Do not build the tests for unsupported features.\n"))
(substitute* "CMakeLists.txt"
- (("add_subdirectory\\(unsupported\\)")
- "# Do not build the tests for unsupported features.\n")
;; Work around
;; <http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1114>.
(("\"include/eigen3\"")
--
2.17.0
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K
K
Kei Kebreau wrote on 29 May 2018 22:55
(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
87h8mqkwq0.fsf@posteo.net
Kei Kebreau <kkebreau@posteo.net> writes:

Toggle quote (28 lines)
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> Hi Kei,
>>
>> please also note that Shogun contains references to proprietary
>> software. It has support for SVMLight, which is non-free software. It
>> includes a script to remove all references to and adapters for SVMLight,
>> but unfortunately we cannot run shell scripts in a snippet. Changing
>> this requires changing the “package” syntax to delay evaluation more.
>>
>> Until then we need to remove the non-free bits in code, which is what
>> the current snippet does, but the code would need to be adjusted for
>> version 6.1.3.
>>
>> Thanks for taking this on!
>>
>> --
>> Ricardo
>
> Thank you for the tip!
>
> I've attached the four patches that make it possible to build Shogun
> 6.1.3 successfully, and I'm just looking through the source code to
> remove the proprietary bits.
>
> P.S. Ricardo, you'll notice the eigen patch is actually yours from
> another patchset! I verified that it works as expected.

The shogun patch below builds successfully for me! If no corrections
need to be made, I'll push this patch series to master!
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R
R
Ricardo Wurmus wrote on 29 May 2018 23:32
(name . Kei Kebreau)(address . kkebreau@posteo.net)
878t82qhai.fsf@mdc-berlin.de
Kei Kebreau <kkebreau@posteo.net> writes:
Toggle quote (3 lines)
> The shogun patch below builds successfully for me! If no corrections
> need to be made, I'll push this patch series to master!

Beautiful! This looks good to me.

Thank you for making the extra effort even though you just wanted to
update Octave!

--
Ricardo
K
K
Kei Kebreau wrote on 30 May 2018 00:34
(name . Ricardo Wurmus)(address . ricardo.wurmus@mdc-berlin.de)
87d0xeks4x.fsf@posteo.net
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

Toggle quote (9 lines)
> Kei Kebreau <kkebreau@posteo.net> writes:
>> The shogun patch below builds successfully for me! If no corrections
>> need to be made, I'll push this patch series to master!
>
> Beautiful! This looks good to me.
>
> Thank you for making the extra effort even though you just wanted to
> update Octave!

Packaging things like this makes for a great puzzle, and I love puzzles.

Pushed to master! Thanks to everyone involved in the review!
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L
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Ludovic Courtès wrote on 31 May 2018 17:41
control message for bug #31479
(address . control@debbugs.gnu.org)
876033omru.fsf@gnu.org
tags 31479 fixed
close 31479
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