GNU bug report logs

#31479 [PATCH 1/3] gnu: octave: Update to 4.4.0.

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Report forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Wed, 16 May 2018 23:12:01 GMT) (full text, mbox, link).

Acknowledgement sent to Kei Kebreau <kkebreau@posteo.net>:
New bug report received and forwarded. Copy sent to guix-patches@gnu.org. (Wed, 16 May 2018 23:12:01 GMT) (full text, mbox, link).

Message #5 received at submit@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: guix-patches@gnu.org
Cc: Kei Kebreau <kkebreau@posteo.net>
Subject: [PATCH 1/3] gnu: octave: Update to 4.4.0.
Date: Wed, 16 May 2018 19:10:33 -0400
* gnu/packages/maths.scm (octave): Update to 4.4.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Wed, 16 May 2018 23:21:02 GMT) (full text, mbox, link).

Message #8 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: 31479@debbugs.gnu.org
Cc: Kei Kebreau <kkebreau@posteo.net>
Subject: [PATCH 2/3] gnu: Add rxcpp.
Date: Wed, 16 May 2018 19:19:56 -0400
* gnu/packages/machine-learning.scm (rxcpp): New variable.
---
 gnu/packages/machine-learning.scm | 42 +++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

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

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Wed, 16 May 2018 23:21:02 GMT) (full text, mbox, link).

Message #11 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: 31479@debbugs.gnu.org
Cc: Kei Kebreau <kkebreau@posteo.net>
Subject: [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Wed, 16 May 2018 19:19:57 -0400
* 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"))
-- 
2.17.0

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Wed, 16 May 2018 23:25:01 GMT) (full text, mbox, link).

Message #14 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: 31479@debbugs.gnu.org
Subject: Re: [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Wed, 16 May 2018 19:24:01 -0400
[Message part 1 (text/plain, inline)]
Kei Kebreau <kkebreau@posteo.net> writes:

> * 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?

[signature.asc (application/pgp-signature, inline)]

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Thu, 17 May 2018 11:25:02 GMT) (full text, mbox, link).

Message #17 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: ludo@gnu.org (Ludovic Courtès)
To: Kei Kebreau <kkebreau@posteo.net>
Cc: 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 1/3] gnu: octave: Update to 4.4.0.
Date: Thu, 17 May 2018 13:24:23 +0200
Kei Kebreau <kkebreau@posteo.net> skribis:

> * gnu/packages/maths.scm (octave): Update to 4.4.0.

LGTM, thanks!

Ludo'.

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Thu, 17 May 2018 11:27:02 GMT) (full text, mbox, link).

Message #20 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: ludo@gnu.org (Ludovic Courtès)
To: Kei Kebreau <kkebreau@posteo.net>
Cc: 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 2/3] gnu: Add rxcpp.
Date: Thu, 17 May 2018 13:26:01 +0200
Kei Kebreau <kkebreau@posteo.net> skribis:

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

[...]

> +    (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’.

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Thu, 17 May 2018 11:40:02 GMT) (full text, mbox, link).

Message #23 received at submit@debbugs.gnu.org (full text, mbox, reply):

From: Jonathan Brielmaier <jonathan.brielmaier@web.de>
To: guix-patches@gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Thu, 17 May 2018 13:39:07 +0200
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 :)

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Fri, 18 May 2018 06:00:01 GMT) (full text, mbox, link).

Message #26 received at submit@debbugs.gnu.org (full text, mbox, reply):

From: Jonathan Brielmaier <jonathan.brielmaier@web.de>
To: guix-patches@gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Fri, 18 May 2018 07:58:50 +0200
[Message part 1 (text/plain, inline)]
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...




[shogun_build.txt (text/plain, attachment)]

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Fri, 18 May 2018 17:10:01 GMT) (full text, mbox, link).

Message #29 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: Jonathan Brielmaier <jonathan.brielmaier@web.de>
Cc: 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Fri, 18 May 2018 13:08:57 -0400
[Message part 1 (text/plain, inline)]
Jonathan Brielmaier <jonathan.brielmaier@web.de> 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 (text/plain, attachment)]
[signature.asc (application/pgp-signature, inline)]

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Sat, 19 May 2018 20:19:01 GMT) (full text, mbox, link).

Message #32 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: ludo@gnu.org (Ludovic Courtès)
To: Kei Kebreau <kkebreau@posteo.net>
Cc: Ricardo Wurmus <rekado@elephly.net>, Jonathan Brielmaier <jonathan.brielmaier@web.de>, 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Sat, 19 May 2018 22:18:02 +0200
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’.

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Sun, 20 May 2018 18:33:02 GMT) (full text, mbox, link).

Message #35 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: ludo@gnu.org (Ludovic Courtès)
Cc: Ricardo Wurmus <rekado@elephly.net>, Jonathan Brielmaier <jonathan.brielmaier@web.de>, 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Sun, 20 May 2018 14:31:48 -0400
[Message part 1 (text/plain, inline)]
ludo@gnu.org (Ludovic Courtès) writes:

> 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.

[signature.asc (application/pgp-signature, inline)]

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Thu, 24 May 2018 09:10:02 GMT) (full text, mbox, link).

Message #38 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Kei Kebreau <kkebreau@posteo.net>
Cc: 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Thu, 24 May 2018 11:09:09 +0200
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

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Sun, 27 May 2018 01:23:01 GMT) (full text, mbox, link).

Message #41 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: ludo@gnu.org, 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Sat, 26 May 2018 21:21:43 -0400
[Message part 1 (text/plain, inline)]
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.

[0001-gnu-octave-Update-to-4.4.0.patch (text/plain, attachment)]
[0002-gnu-Add-rxcpp.patch (text/plain, attachment)]
[0003-gnu-eigen-Include-unsupported-features.patch (text/plain, attachment)]
[0004-gnu-swig-Patch-for-Octave-4.4.patch (text/plain, attachment)]
[signature.asc (application/pgp-signature, inline)]

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Tue, 29 May 2018 20:57:01 GMT) (full text, mbox, link).

Message #44 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: ludo@gnu.org, 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Tue, 29 May 2018 16:55:51 -0400
[Message part 1 (text/plain, inline)]
Kei Kebreau <kkebreau@posteo.net> writes:

> 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!


[0005-gnu-Update-shogun-to-6.1.3.patch (text/plain, attachment)]
[signature.asc (application/pgp-signature, inline)]

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Tue, 29 May 2018 21:33:01 GMT) (full text, mbox, link).

Message #47 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Kei Kebreau <kkebreau@posteo.net>
Cc: ludo@gnu.org, 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Tue, 29 May 2018 23:32:37 +0200
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!

-- 
Ricardo

Information forwarded to guix-patches@gnu.org:
bug#31479; Package guix-patches. (Tue, 29 May 2018 22:36:01 GMT) (full text, mbox, link).

Message #50 received at 31479@debbugs.gnu.org (full text, mbox, reply):

From: Kei Kebreau <kkebreau@posteo.net>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: ludo@gnu.org, jonathan.brielmaier@web.de, 31479@debbugs.gnu.org
Subject: Re: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.
Date: Tue, 29 May 2018 18:34:54 -0400
[Message part 1 (text/plain, inline)]
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> 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!

[signature.asc (application/pgp-signature, inline)]

Added tag(s) fixed. Request was from ludo@gnu.org (Ludovic Courtès) to control@debbugs.gnu.org. (Thu, 31 May 2018 15:42:01 GMT) (full text, mbox, link).

bug closed, send any further explanations to 31479@debbugs.gnu.org and Kei Kebreau <kkebreau@posteo.net> Request was from ludo@gnu.org (Ludovic Courtès) to control@debbugs.gnu.org. (Thu, 31 May 2018 15:42:01 GMT) (full text, mbox, link).

bug archived. Request was from Debbugs Internal Request <help-debbugs@gnu.org> to internal_control@debbugs.gnu.org. (Fri, 29 Jun 2018 11:24:05 GMT) (full text, mbox, link).

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