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eric-wieser opened this issue Jul 14, 2017 · 6 comments · Fixed by #10074
Closed

Build errors with existing qhull #8872

eric-wieser opened this issue Jul 14, 2017 · 6 comments · Fixed by #10074

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@eric-wieser
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eric-wieser commented Jul 14, 2017 •
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Having trouble building matplotlib from source. It seems that QHULL_LIB_CHECK is not defined for me, which causes a chain of useless errors. My guess is that the problem is I already have a system Qhull package (for ROS), which is conflicting with the bundled one. Here's the output I get:

python setup.py build 
============================================================================
Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
            matplotlib: yes [2.0.2+4383.g4690576]
                python: yes [2.7.6 (default, Oct 26 2016, 20:30:19)  [GCC
                        4.8.4]]
              platform: yes [linux2]

REQUIRED DEPENDENCIES AND EXTENSIONS
                 numpy: yes [version 1.8.2]
                   six: yes [using six version 1.10.0]
              dateutil: yes [using dateutil version 1.5]
backports.functools_lru_cache: yes [backports.functools_lru_cache was not
                        found. It is required forPython versions prior to
                        3.2]
          subprocess32: yes [subprocess32 was not found. It used  for Python
                        versions prior to 3.2 to improves functionality on
                        Linux and OSX]
                  pytz: yes [using pytz version 2012c]
                cycler: yes [cycler was not found. pip/easy_install may
                        attempt to install it after matplotlib.]
               tornado: yes [tornado was not found. It is required for the
                        WebAgg backend. pip/easy_install may attempt to
                        install it after matplotlib.]
             pyparsing: yes [using pyparsing version 2.1.10]
                libagg: yes [pkg-config information for 'libagg' could not
                        be found. Using local copy.]
              freetype: yes [Using local version for testing]
                   png: yes [version 1.2.50]
                 qhull: yes [Using system Qhull (version unknown, no pkg-
                        config info)]

OPTIONAL SUBPACKAGES
           sample_data: yes [installing]
              toolkits: yes [installing]
                 tests: no  [skipping due to configuration]
        toolkits_tests: no  [skipping due to configuration]

OPTIONAL BACKEND EXTENSIONS
                macosx: no  [Mac OS-X only]
                qt5agg: no  [PySide2 not found; PyQt5 not found]
                qt4agg: yes [installing, Qt: 4.8.6, PySide: 1.2.1; Qt:
                        4.8.6, PyQt: 4.8.6]
               gtk3agg: no  [Requires gtk3 development files to be
                        installed.]
             gtk3cairo: no  [Requires gtk3 development files to be
                        installed.]
/usr/lib/python2.7/dist-packages/gtk-2.0/gtk/__init__.py:57: GtkWarning: could not open display
  warnings.warn(str(e), _gtk.Warning)
                gtkagg: no  [The C/C++ header for pygtk (pygtk/pygtk.h)
                        could not be found.  You may need to install the
                        development package.]
                 tkagg: yes [installing; run-time loading from Python Tcl /
                        Tk]
                 wxagg: yes [installing, version 2.8.12.1]
                   gtk: no  [The C/C++ header for pygtk (pygtk/pygtk.h)
                        could not be found.  You may need to install the
                        development package.]
                   agg: yes [installing]
                 cairo: yes [installing, pycairo version 1.8.8]
             windowing: no  [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES
                dvipng: no
           ghostscript: yes [version 9.10]
                 latex: yes [version 3.1415926]
               pdftops: no

OPTIONAL PACKAGE DATA
                  dlls: no  [skipping due to configuration]

running build
running build_py
copying lib/matplotlib/mpl-data/matplotlibrc -> build/lib.linux-x86_64-2.7/matplotlib/mpl-data
UPDATING build/lib.linux-x86_64-2.7/matplotlib/_version.py
set build/lib.linux-x86_64-2.7/matplotlib/_version.py to '2.0.2+4383.g4690576'
running build_ext
building 'matplotlib._qhull' extension
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC -DMPL_DEVNULL=/dev/null -DPY_ARRAY_UNIQUE_SYMBOL=MPL_matplotlib__qhull_ARRAY_API -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -D__STDC_FORMAT_MACROS=1 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/usr/include/python2.7 -c src/qhull_wrap.c -o build/temp.linux-x86_64-2.7/src/qhull_wrap.o
src/qhull_wrap.c: In function ‘delaunay_impl’:
src/qhull_wrap.c:112:5: error: unknown type name ‘QHULL_LIB_CHECK’
     QHULL_LIB_CHECK
     ^
src/qhull_wrap.c:115:5: error: conflicting types for ‘points’
     points = (coordT*)malloc(npoints*ndim*sizeof(coordT));
     ^
src/qhull_wrap.c:96:13: note: previous definition of ‘points’ was here
     coordT* points = NULL;
             ^
src/qhull_wrap.c:115:14: warning: initialization makes integer from pointer without a cast [enabled by default]
     points = (coordT*)malloc(npoints*ndim*sizeof(coordT));
              ^
src/qhull_wrap.c:116:16: warning: comparison between pointer and integer [enabled by default]
     if (points == NULL) {
                ^
src/qhull_wrap.c:124:15: error: subscripted value is neither array nor pointer nor vector
         points[2*i  ] = x[i];
               ^
src/qhull_wrap.c:125:15: error: subscripted value is neither array nor pointer nor vector
         points[2*i+1] = y[i];
               ^
src/qhull_wrap.c:147:29: warning: passing argument 3 of ‘qh_new_qhull’ makes pointer from integer without a cast [enabled by default]
                             "qhull d Qt Qbb Qc Qz", NULL, error_file);
                             ^
In file included from /usr/include/libqhull/qhull_a.h:27:0,
                 from src/qhull_wrap.c:10:
/usr/include/libqhull/libqhull.h:1002:9: note: expected ‘double *’ but argument is of type ‘int’
 int     qh_new_qhull(int dim, int numpoints, coordT *points, boolT ismalloc,
         ^
src/qhull_wrap.c:230:5: warning: passing argument 1 of ‘free’ makes pointer from integer without a cast [enabled by default]
     free(points);
     ^
In file included from /usr/include/python2.7/Python.h:42:0,
                 from src/qhull_wrap.c:8:
/usr/include/stdlib.h:483:13: note: expected ‘void *’ but argument is of type ‘int’
 extern void free (void *__ptr) __THROW;
             ^
src/qhull_wrap.c:249:5: warning: passing argument 1 of ‘free’ makes pointer from integer without a cast [enabled by default]
     free(points);
     ^
In file included from /usr/include/python2.7/Python.h:42:0,
                 from src/qhull_wrap.c:8:
/usr/include/stdlib.h:483:13: note: expected ‘void *’ but argument is of type ‘int’
 extern void free (void *__ptr) __THROW;
             ^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

In case it's relevant, here's some info about my installed qhull

dpkg -s libqhull-dev 
Package: libqhull-dev
Status: install ok installed
Priority: optional
Section: libdevel
Installed-Size: 1092
Maintainer: Ubuntu Developers <[email protected]>
Architecture: amd64
Multi-Arch: same
Source: qhull
Version: 2012.1-4
Depends: libqhull6 (= 2012.1-4)
Description: calculate convex hulls and related structures (development files)
 Qhull computes convex hulls, Delaunay triangulations, halfspace
 intersections about a point, Voronoi diagrams, furthest-site
 Delaunay triangulations, and furthest-site Voronoi diagrams. It
 runs in 2-d, 3-d, 4-d, and higher dimensions.
 .
 This package contains the files necessary for development (headers and
 libraries), as well as the library documentation in HTML format.
Original-Maintainer: Debian Science Maintainers <[email protected]>
Homepage: http://www.qhull.org

I'm doing this on WSL.
@eric-wieser
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eric-wieser commented Jul 14, 2017 •
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The installation instructions say qhull 2012.1 is correct, yet matplotlib is actually bundled with 2015.2.

This looks like a documentation bug to me

Edit: That's actually just the difference between master and release, so everything is fine

@eric-wieser
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eric-wieser commented Jul 14, 2017 •
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qhull 2015.2 is not available on ubuntu 14.04 - so how can I tell matplotlib to use its bundled version, and not the system version?

@eric-wieser
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eric-wieser commented Jul 14, 2017 •
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So, this seems like a bug to me, in setupext

        try:
            # fails if the version is too old
            return self._check_for_pkg_config(
                'libqhull', 'libqhull/qhull_a.h', min_version='2015.2')
        except CheckFailed as e:
            use_the_old_version_anyway()

Surely if the version doesn't match, we should use the bundled qhull?

@renxinhe
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I ran into similar issue with qhull, and fixed it by manually updating libqhull-dev from 2012 to 2015. You can find the .deb files on this website.

I have a Ubuntu 14.04 machine running on Intel i5 processor, so I installed dependency libqhull7_2015.2-2_amd64.deb first, and then updated qhull with libqhull-dev_2015.2-2_amd64.deb.

Finally, I ran pip3 install matplotlib and the error went away.

@eric-wieser
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Still seems strange for matplotlib to bundle qhull, yet not use it when it needs to

@anntzer
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anntzer commented Oct 19, 2017

see #8390 (comment) for the rationale (which I definitely agree is not very strong).

@anntzer anntzer mentioned this issue Dec 22, 2017
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@MichaelGrupp MichaelGrupp mentioned this issue Jan 4, 2018
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Prefer vendored qhull if sys-wide version can't be determined. anntzer/matplotlib
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@eric-wieser @anntzer @renxinhe