Control: tags -1 patch fixed-upstream
On Sat, Dec 26, 2020 at 10:45:50PM +0100, Lucas Nussbaum wrote:
> Source: swiglpk
> Version: 4.65.0-2
> Severity: serious
> Justification: FTBFS on amd64
> Tags: bullseye sid ftbfs
> Usertags: ftbfs-20201226 ftbfs-bullseye
>...
> > ======================================================================
> > ERROR: Failure: ImportError
> > (/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_swiglpk/build/swiglpk/_swiglpk.cpython-39-x86_64-linux-gnu.so:
> > undefined symbol: glp_netgen_prob)
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> > File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
> > raise self.exc_val.with_traceback(self.tb)
> > File "/usr/lib/python3/dist-packages/nose/loader.py", line 416, in
> > loadTestsFromName
> > module = self.importer.importFromPath(
> > File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in
> > importFromPath
> > return self.importFromDir(dir_path, fqname)
> > File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in
> > importFromDir
> > mod = load_module(part_fqname, fh, filename, desc)
> > File "/usr/lib/python3.9/imp.py", line 244, in load_module
> > return load_package(name, filename)
> > File "/usr/lib/python3.9/imp.py", line 216, in load_package
> > return _load(spec)
> > File "<frozen importlib._bootstrap>", line 711, in _load
> > File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
> > File "<frozen importlib._bootstrap_external>", line 790, in exec_module
> > File "<frozen importlib._bootstrap>", line 228, in
> > _call_with_frames_removed
> > File
> > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_swiglpk/build/swiglpk/__init__.py",
> > line 1, in <module>
> > from .swiglpk import *
> > File
> > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_swiglpk/build/swiglpk/swiglpk.py",
> > line 13, in <module>
> > from . import _swiglpk
> > ImportError:
> > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_swiglpk/build/swiglpk/_swiglpk.cpython-39-x86_64-linux-gnu.so:
> > undefined symbol: glp_netgen_prob
> >
> > ----------------------------------------------------------------------
>...
Attached are the relevant parts from the upstream fix.
After that, it is worth trying whether this fixed python-cobra.
cu
Adrian
>From ec985c15ae507139de70b943c56f1042acd79a8a Mon Sep 17 00:00:00 2001
From: Jonathon Fletcher <jonathon.fletc...@gmail.com>
Date: Tue, 2 Feb 2021 00:56:27 -0800
Subject: ignore problematic functions via swig directives in glpk.i (#43)
diff --git a/scripts/find_newest_glpk_release.py b/scripts/find_newest_glpk_release.py
index bf79f74..e4254df 100755
--- a/scripts/find_newest_glpk_release.py
+++ b/scripts/find_newest_glpk_release.py
@@ -12,7 +12,8 @@ if response.ok:
new_major, new_minor = int(match[0][0]), int(match[0][1])
if new_major > major:
major = new_major
- if new_minor > minor:
+ minor = new_minor
+ if new_major >= major and new_minor > minor:
minor = new_minor
print('{}.{}'.format(major, minor), end='')
diff --git a/setup.py b/setup.py
index fbf76a1..e8d81b1 100644
--- a/setup.py
+++ b/setup.py
@@ -22,39 +22,38 @@ from distutils.command.build import build
import subprocess
import versioneer
-def copy_glpk_header():
- if os.path.isfile('glpk.h'):
+
+def find_glpk_header():
+ if os.environ.get("GLPK_HEADER_PATH", None) and os.path.isdir(os.environ.get("GLPK_HEADER_PATH", None)):
+ print('glpk.h found in GLPK_HEADER_PATH environment variable')
+ glpk_header_path = os.path.join(os.environ.get("GLPK_HEADER_PATH", None), 'glpk.h')
+ elif os.path.isfile('glpk.h'):
print('glpk.h found in source directory')
- glpk_header_path = os.path.join('./', 'glpk.h')
+ glpk_header_path = os.path.join(os.getcwd(), 'glpk.h')
else:
print('Trying to determine glpk.h location')
- glpsol_path = os.path.dirname(subprocess.check_output(['which', 'glpsol']))
- glpk_header_path = os.path.join(os.path.dirname(glpsol_path).decode("utf-8"), 'include', 'glpk.h')
- print('glpk.h found at {}'.format(glpk_header_path))
+ glpsol_dirname = os.path.dirname(subprocess.check_output(['which', 'glpsol']))
+ glpk_header_path = os.path.join(os.path.dirname(glpsol_dirname).decode("utf-8"), 'include', 'glpk.h')
if os.path.exists(glpk_header_path):
- with open('swiglpk/glpk_clean.h', 'w') as out_handle:
- with open(glpk_header_path) as in_handle:
- for line in in_handle:
- if line == 'void glp_vprintf(const char *fmt, va_list arg);\n':
- out_handle.write('// The following line is commented out because it is causing problems with swig\n')
- out_handle.write('// void glp_vprintf(const char *fmt, va_list arg);')
- else:
- out_handle.write(line)
+ print('glpk.h found at {}'.format(glpk_header_path))
+ return os.path.dirname(os.path.abspath(glpk_header_path))
else:
raise Exception('Could not find glpk.h! Maybe glpk or glpsol is not installed.')
+
try:
with open('README.rst', 'r') as f:
long_description = f.read()
-except:
+except Exception:
long_description = ''
-# Copy and process glpk.h into current directory
-copy_glpk_header()
+glpk_header_dirname = find_glpk_header()
+
custom_cmd_class = versioneer.get_cmdclass()
+
class CustomBuild(build):
sub_commands = [
('build_ext', build.has_ext_modules),
@@ -63,6 +62,7 @@ class CustomBuild(build):
('build_scripts', build.has_scripts),
]
+
custom_cmd_class['build'] = CustomBuild
try:
@@ -102,6 +102,8 @@ setup(
],
ext_modules=[Extension("swiglpk._swiglpk",
sources=["swiglpk/glpk.i"],
+ include_dirs=[glpk_header_dirname],
+ swig_opts=["-I"+glpk_header_dirname],
libraries=['glpk'])],
include_package_data=True
)
diff --git a/swiglpk/__init__.py b/swiglpk/__init__.py
index 3b10d42..5bc73ae 100644
--- a/swiglpk/__init__.py
+++ b/swiglpk/__init__.py
@@ -1 +1 @@
-from .swiglpk import *
\ No newline at end of file
+from .swiglpk import *
diff --git a/swiglpk/glpk.i b/swiglpk/glpk.i
index 0ede927..ade8fbb 100644
--- a/swiglpk/glpk.i
+++ b/swiglpk/glpk.i
@@ -16,11 +16,14 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
+%ignore glp_vprintf;
+%ignore glp_netgen_prob;
+
%module swiglpk
%{
#define SWIG_FILE_WITH_INIT
-#include "./glpk_clean.h"
+#include "glpk.h"
int wrap_glp_term_hook_cb(void *info, const char *s)
{
@@ -61,7 +64,7 @@ PyObject *wrap_glp_term_hook(PyObject *callback)
}
%}
-%include glpk_clean.h
+%include glpk.h
%include "carrays.i"
%array_class(int, intArray);
