Re: 04/05: gnu: swig: Patch for Octave 4.4.

[Kei Kebreau <kkebreau@posteo.net>]

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Kei Kebreau <kkebreau@posteo.net> writes:

> Other than Shogun's Python/SWIG-related build failure (attached), this
> patch seems to work fairly well. There appears to be an upstream issue
> related to the invalid conversion mentioned in the build failure. I'm
> keeping an eye on it for any new developments.

FYI, this is an updated patch that bypasses the Python interface issue
and runs into an issue with R.


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From f4fa63249bec73a385bba1b95bc53cac8f96420c Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Wed, 30 May 2018 08:34:42 -0400
Subject: [PATCH] gnu: shogun: Use a patched swig for Octave 4.4.

* gnu/packages/swig.scm (swig-git): New variable
* gnu/packages/machine-learning.scm (shogun)[arguments]: Add
'fix-python-compiler-flags' phase.
[inputs]: Replace swig with swig-git.
---
 gnu/packages/machine-learning.scm |  9 +++++++-
 gnu/packages/swig.scm             | 34 +++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 15e4d4574..d992a2fe5 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -469,6 +469,13 @@ sample proximities between pairs of cases.")
                (mkdir-p rxcpp-dir)
                (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
                #t)))
+         (add-after 'unpack 'fix-python-compiler-flags
+           (lambda _
+             ;; This prevents a set of function conversions from stopping the
+             ;; build with an error.
+             (substitute* "src/interfaces/python/CMakeLists.txt"
+               (("Wno-c\\+\\+11-narrowing") "fpermissive"))
+             #t))
          (add-before 'build 'set-HOME
            ;; $HOME needs to be set at some point during the build phase
            (lambda _ (setenv "HOME" "/tmp") #t)))
@@ -488,7 +495,7 @@ sample proximities between pairs of cases.")
        ("numpy" ,python-numpy)
        ("r-minimal" ,r-minimal)
        ("octave" ,octave)
-       ("swig" ,swig)
+       ("swig" ,swig-git)
        ("eigen" ,eigen)
        ("hdf5" ,hdf5)
        ("atlas" ,atlas)
diff --git a/gnu/packages/swig.scm b/gnu/packages/swig.scm
index b931db412..3a1139dbb 100644
--- a/gnu/packages/swig.scm
+++ b/gnu/packages/swig.scm
@@ -20,8 +20,12 @@
 (define-module (gnu packages swig)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix licenses)
+  #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages boost)
@@ -74,3 +78,33 @@ you tailor the wrapping process to suit your application.")
 
     ;; See http://www.swig.org/Release/LICENSE for details.
     (license gpl3+)))
+
+;; This package contains upstream fixes that haven't been released as part of a
+;; stable version of SWIG.  This is necessary for software that uses SWIG to
+;; compile the correct and up-to-date programming language interfaces.
+(define-public swig-git
+  (let ((commit "12c66f9b7d884020e896ce92b9783bc3bac95d2d")
+        (revision "1"))
+    (package/inherit swig
+      (name "swig-git")
+      (version (git-version "4.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/swig/swig.git")
+               (commit commit)))
+         (sha256 (base32 "1367y47kdkly9cwyp4d60cm5d660am83g4p52k1hmzvimghwgvlp"))
+         (file-name (git-file-name name version))))
+      (arguments
+       (substitute-keyword-arguments (package-arguments swig)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'unpack 'autogen
+               (lambda _
+                 (invoke "sh" "autogen.sh")))))))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("bison" ,bison)
+         ,@(package-native-inputs swig))))))
-- 
2.17.1


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[ 79%] Linking CXX shared module shogun.so
cd /tmp/guix-build-shogun-6.1.3.drv-0/build/src/interfaces/r && /gnu/store/8mycww9vx11vidzka3g5gghwq11alk4w-cmake-3.7.2/bin/cmake -E cmake_link_script CMakeFiles/interface_r.dir/link.txt --verbose=1
/gnu/store/cfdn69spjc44x4sd0acrwhxq6yay3rbc-gcc-5.5.0/bin/c++  -fPIC -O0 -g  -I/gnu/store/42j0p3x4v2gbwqyx6iv1j83qckndm799-r-minimal-3.5.0/lib/R/include -O2 -g -DNDEBUG  -shared  -o shogun.so CMakeFiles/interface_r.dir/shogunR_wrap.cxx.o CMakeFiles/interface_r.dir/sg_print_functions.cpp.o  -L/gnu/store/42j0p3x4v2gbwqyx6iv1j83qckndm799-r-minimal-3.5.0/lib/R/lib -Wl,-rpath,/gnu/store/km7w7j4f9qsmnrsag3g94nc6fb20vrxw-shogun-6.1.3/lib:/gnu/store/42j0p3x4v2gbwqyx6iv1j83qckndm799-r-minimal-3.5.0/lib/R/lib ../../shogun/libshogun.so.18.0 -lR -lxml2 -lhdf5 -lz -ldl -lm 
Generating shogun.RData
cd /tmp/guix-build-shogun-6.1.3.drv-0/build/src/interfaces/r && echo 'wd="/tmp/guix-build-shogun-6.1.3.drv-0/build/src/interfaces/r" ; setwd ( wd ) ; f="shogun.R" ; fdata="shogun.RData" ; source ( f ) ; save ( list=ls ( all=TRUE ) , file=fdata , compress=TRUE ) ; q ( save="no" ) ;' | /gnu/store/42j0p3x4v2gbwqyx6iv1j83qckndm799-r-minimal-3.5.0/bin/R --silent --no-save
> wd="/tmp/guix-build-shogun-6.1.3.drv-0/build/src/interfaces/r" ; setwd ( wd ) ; f="shogun.R" ; fdata="shogun.RData" ; source ( f ) ; save ( list=ls ( all=TRUE ) , file=fdata , compress=TRUE ) ; q ( save="no" ) ;
in method for ‘copyToR’ with signature ‘"_p_shogun::BmrmStatistics"’: no definition for class “_p_shogun::BmrmStatistics”
in method for ‘copyToR’ with signature ‘"_p_shogun::CResultSet"’: no definition for class “_p_shogun::CResultSet”
in method for ‘copyToR’ with signature ‘"_p_shogun::CRealNumber"’: no definition for class “_p_shogun::CRealNumber”
in method for ‘copyToR’ with signature ‘"_p_shogun::GCEdge"’: no definition for class “_p_shogun::GCEdge”
in method for ‘copyToR’ with signature ‘"_p_shogun::GCNode"’: no definition for class “_p_shogun::GCNode”
in method for ‘copyToR’ with signature ‘"_p_shogun::GCNodePtr"’: no definition for class “_p_shogun::GCNodePtr”
in method for ‘copyToR’ with signature ‘"_p_shogun::RelaxedTreeNodeData"’: no definition for class “_p_shogun::RelaxedTreeNodeData”
in method for ‘copyToR’ with signature ‘"_p_shogun::ConditionalProbabilityTreeNodeData"’: no definition for class “_p_shogun::ConditionalProbabilityTreeNodeData”
Error in assign(defName, .values, envir = where) : 
  object 'KSM_MAXIMIZE_POWER' not found
  Calls: source ... withVisible -> eval -> eval -> defineEnumeration -> assign
  Execution halted
  make[2]: *** [src/interfaces/r/CMakeFiles/interface_r.dir/build.make:141: src/interfaces/r/shogun.so] Error 1
  make[2]: *** Deleting file 'src/interfaces/r/shogun.so'
  make[2]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build'
  make[1]: *** [CMakeFiles/Makefile2:462: src/interfaces/r/CMakeFiles/interface_r.dir/all] Error 2
  make[1]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build'
  make: *** [Makefile:153: all] Error 2

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