#9221 closed enhancement (fixed)
update matplotlib to 1.0.0 and clean out the patches
Reported by: | Jason Grout | Owned by: | jason, was |
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Priority: | major | Milestone: | sage-4.6 |
Component: | graphics | Keywords: | |
Cc: | David Kirkby, Karl-Dieter Crisman | Merged in: | sage-4.6.alpha3 |
Authors: | Jason Grout | Reviewers: | David Kirkby, Karl-Dieter Crisman |
Report Upstream: | Fixed upstream, but not in a stable release. | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
Matplotlib 1.0.0 has some bugfixes and enhancements that are really nice for us. For example, the configuration variables allow us to eliminate most of our patches to the spkg, and a new path.snap config parameter solves #7808.
The spkg is up at http://sage.math.washington.edu/home/jason/matplotlib-1.0.0.spkg.
Attachments (1)
Change History (93)
comment:1 Changed 12 years ago by
Report Upstream: | N/A → Reported upstream. Little or no feedback. |
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Status: | new → needs_work |
comment:2 Changed 12 years ago by
Status: | needs_work → needs_info |
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comment:3 Changed 12 years ago by
Description: | modified (diff) |
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Report Upstream: | Reported upstream. Little or no feedback. → N/A |
Summary: | update matplotlib to svn and clean out the patches → update matplotlib to 1.0.0 and clean out the patches |
comment:4 Changed 12 years ago by
David, can you check to see if this spkg compiles on Solaris, or if we need to still address the issues at the end of #9202?
comment:5 Changed 12 years ago by
See what's new at: http://matplotlib.sourceforge.net/users/whats_new.html
comment:6 follow-up: 7 Changed 12 years ago by
This was in the log, so I think this should compile on Solaris now:
2010-07-02 Modified CXX/WrapPython.h to fix "swab bug" on solaris so mpl can compile on Solaris with CXX6 in the trunk. Closes tracker bug 3022815 - JDH
comment:7 Changed 12 years ago by
Status: | needs_info → needs_work |
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Replying to jason:
This was in the log, so I think this should compile on Solaris now:
2010-07-02 Modified CXX/WrapPython.h to fix "swab bug" on solaris so mpl can compile on Solaris with CXX6 in the trunk. Closes tracker bug 3022815 - JDH
No such luck. I've tried on both Solaris 10 on SPARC, and OpenSolaris on x64. It looks like a mix of compilation modes is causing them to get two different definitions for swab.
The bug tracker suggests this was a very recent fix, so may not have made it into 1.0. If if did make it into 1.0, then it failed to solve the problem.
Solaris 10 update with Sun UltraSPARC T2+ processors
- Sun T5240
- 2 x 8 core, 64-thread UltraSPARC T2+ 1167 MHz
- 32 GB RAM
- Solaris 10 update 7 (05/09)
- t2.math.washtington.edu
- gcc 4.4.1 configured to use both the Sun linker and assembler.
- A build of sage-4.5.alpha4 was used to test matplotlib-1.0.0.spkg
- MD5 checksum of matplotlib-1.0.0.spkg was cb9f3cb0ec3da550d2d67ea7e8b6094f
- 32-bit build (This is the default). The environment variable
SAGE64
was not used.
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/tmp/kirkby/sage-4.5.alpha4/local/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/tmp/kirkby/sage-4.5.alpha4/local/include/freetype2 -I/tmp/kirkby/sage-4.5.alpha4/local/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/include/python2.6 -c agg24/src/agg_vcgen_dash.cpp -o build/temp.solaris-2.10-sun4v-2.6/agg24/src/agg_vcgen_dash.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/tmp/kirkby/sage-4.5.alpha4/local/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/tmp/kirkby/sage-4.5.alpha4/local/include/freetype2 -I/tmp/kirkby/sage-4.5.alpha4/local/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/include/python2.6 -c agg24/src/agg_image_filters.cpp -o build/temp.solaris-2.10-sun4v-2.6/agg24/src/agg_image_filters.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/tmp/kirkby/sage-4.5.alpha4/local/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/tmp/kirkby/sage-4.5.alpha4/local/include/freetype2 -I/tmp/kirkby/sage-4.5.alpha4/local/include -I. -I/tmp/kirkby/sage-4.5.alpha4/local/include/python2.6 -c src/backend_agg.cpp -o build/temp.solaris-2.10-sun4v-2.6/src/backend_agg.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from /tmp/kirkby/sage-4.5.alpha4/local/include/python2.6/Python.h:8, from ./CXX/WrapPython.h:61, from ./CXX/Extensions.hxx:37, from src/ft2font.h:4, from src/backend_agg.cpp:10: /tmp/kirkby/sage-4.5.alpha4/local/include/python2.6/pyconfig.h:1013:1: warning: "_FILE_OFFSET_BITS" redefined In file included from /usr/include/sys/types.h:18, from /tmp/kirkby/sage-4.5.alpha4/local/include/zconf.h:364, from /tmp/kirkby/sage-4.5.alpha4/local/include/zlib.h:34, from /tmp/kirkby/sage-4.5.alpha4/local/include/png.h:470, from src/backend_agg.cpp:3: /usr/local/gcc-4.4.1-sun-linker/bin/../lib/gcc/sparc-sun-solaris2.10/4.4.1/include-fixed/sys/feature_tests.h:197:1: warning: this is the location of the previous definition In file included from /tmp/kirkby/sage-4.5.alpha4/local/include/python2.6/Python.h:42, from ./CXX/WrapPython.h:61, from ./CXX/Extensions.hxx:37, from src/ft2font.h:4, from src/backend_agg.cpp:10: /usr/include/stdlib.h:144: error: declaration of C function ‘void swab(const char*, char*, ssize_t)’ conflicts with /usr/include/unistd.h:496: error: previous declaration ‘void swab(const void*, void*, ssize_t)’ here error: command 'gcc' failed with exit status 1 Error building matplotlib package. real 3m35.224s user 3m20.924s sys 0m9.504s sage: An error occurred while installing matplotlib-1.0.0
OpenSolaris 2009.06 on x64 hardware
- Sun Ultra 27
- 1 x 3.33 GHz Intel W3580 Xeon. Quad core. 8 threads.
- 12 GB RAM
- OpenSolaris 2009.06 snv_134 X86
- gcc 4.4.4 configured to use the Sun linker and GNU assembler.
- A build of sage-4.5.alpha4 was used to test matplotlib-1.0.0.spkg
- 64-bit build. OpenSolaris defaults to 32-bit, but the environment variable
SAGE64=yes
was used. - MD5 checksum of matplotlib-1.0.0.spkg was cb9f3cb0ec3da550d2d67ea7e8b6094f
gcc -DNDEBUG -g -O3 -m64 -Wall -Wstrict-prototypes -O2 -g -m64 -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/export/home/drkirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/export/home/drkirkby/sage-4.5.alpha4/local/include -I. -I/export/home/drkirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/export/home/drkirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include -I/export/home/drkirkby/sage-4.5.alpha4/local/include -I. -I/export/home/drkirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include/freetype2 -I/export/home/drkirkby/sage-4.5.alpha4/local/include/freetype2 -I./freetype2 -I/export/home/drkirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include/freetype2 -Isrc/freetype2 -Iagg24/include/freetype2 -I./freetype2 -I/export/home/drkirkby/sage-4.5.alpha4/local/lib/python2.6/site-packages/numpy/core/include/freetype2 -I/export/home/drkirkby/sage-4.5.alpha4/local/include/freetype2 -I./freetype2 -I/export/home/drkirkby/sage-4.5.alpha4/local/include/python2.6 -c src/backend_agg.cpp -o build/temp.solaris-2.11-i86pc-2.6/src/backend_agg.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from /export/home/drkirkby/sage-4.5.alpha4/local/include/python2.6/Python.h:42, from ./CXX/WrapPython.h:61, from ./CXX/Extensions.hxx:37, from src/ft2font.h:4, from src/backend_agg.cpp:10: /usr/include/stdlib.h:159: error: declaration of C function 'void swab(const char*, char*, ssize_t)' conflicts with /usr/include/unistd.h:513: error: previous declaration 'void swab(const void*, void*, ssize_t)' here src/backend_agg.cpp: In member function 'Py::Object RendererAgg::draw_markers(const Py::Tuple&)': src/backend_agg.cpp:727: warning: dereferencing type-punned pointer will break strict-aliasing rules src/backend_agg.cpp:727: warning: dereferencing type-punned pointer will break strict-aliasing rules src/backend_agg.cpp:763: warning: dereferencing type-punned pointer will break strict-aliasing rules src/backend_agg.cpp:763: warning: dereferencing type-punned pointer will break strict-aliasing rules error: command 'gcc' failed with exit status 1 Error building matplotlib package. real 0m19.778s user 0m17.826s sys 0m1.441s sage: An error occurred while installing matplotlib-1.0.0
comment:8 Changed 12 years ago by
Well, the log I posted was from the changelog for 1.0.0, so it certainly look like the fix had made it in. I'll try looking at this soon.
Also, the spkg I posted above needs:
- an updated SPKG.txt file
- long doctests run
before it is officially ready for review.
comment:9 Changed 12 years ago by
David,
I verified that the md5 you reported is for the right spkg and contains the fix. If you have time, could you download the vanilla matplotlib source and try compiling that, just to make sure it isn't a problem with the Sage environment? The 1.0.0 source is here:
https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0/ (I can't test this URL; it isn't loading for me...)
The installation instructions are here:
http://matplotlib.sourceforge.net/users/installing.html
and basically are:
cd matplotlib python setup.py build python setup.py install
I've also posted a report to https://sourceforge.net/mailarchive/forum.php?thread_name=4C349BDE.4020604%40creativetrax.com&forum_name=matplotlib-devel
comment:10 Changed 12 years ago by
Report Upstream: | N/A → Reported upstream. Developers acknowledge bug. |
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comment:11 Changed 12 years ago by
The patch at #9211 (correcting behavior where vertices in graphs are clipped) depends on this spkg.
comment:12 Changed 12 years ago by
The patch needs to be applied so that axes labels come out okay. Compare the results of
plot(x, (x,-3,3), axes_labels=['x','y'])
before and after to check this.
comment:13 Changed 12 years ago by
David,
Could you test compiling the vanilla matplotlib 1.0 source on solaris to see if the issue is in the vanilla upstream package?
Just download from http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0/matplotlib-1.0.0.tar.gz/download
Then untar and do:
cd matplotlib python setup.py build python setup.py install
(or use sage -python
if you want to install into a Sage version of python).
comment:14 Changed 12 years ago by
For reference, here is the mailing list post where John Hunter discusses the fix that he hoped fixed the bug: http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg17531.html
comment:15 Changed 12 years ago by
It's not so easy to test the upstream source code directly, as there are dependencies which are not provided on Solaris. On 't2.math' I get:
kirkby@t2:32 ~/matplotlib-1.0.0$ python setup.py build basedirlist is: ['/usr/local'] ============================================================================ BUILDING MATPLOTLIB matplotlib: 1.0.0 python: 2.4.4 (#1, Jan 10 2007, 01:25:01) [C] platform: sunos5 REQUIRED DEPENDENCIES numpy: no * You must install numpy 1.1 or later to build * matplotlib.
But Numpy has a whole list of dependencies of its own, so I don't want to spend a long time setting that lot up.
But I just retried your .spkg on 't2' using a working copy of the latest sage-4.5.3.alpha0
and find exactly the same problem.
I also tried on my OpenSolaris machine inside a slightly modified version of sage-4.5.3.alpha0
. Again, I get the same problem as before.
To me this looks like an upstream bug, and not anything introduced in Sage.
I just checked the source code, and see the code is actually in matplotlib-1.0.0.
// Prevent multiple conflicting definitions of swab from stdlib.h and unistd.h #if defined(__sun) || defined(sun) #if defined(_XPG4) #undef _XPG4 #endif #if defined(_XPG3) #undef _XPG3 #endif #endif
It seems a bit of a hack to me. If _XPG4
or _XPG3
are defined, there were defined for good reason, and I doubt simply undefining them is the right way to tackle this. I could imagine this could cause a whole lot more problems than it solves.
According to http://en.wikipedia.org/wiki/X/Open the Single UNIX Specification was based on the XPG4 standard, so I would not be surprised that undefining _XPG4
will cause problems as the behavior of hundreds of header files will be changed.
comment:16 follow-up: 18 Changed 12 years ago by
BTW, it perfectly possible on Solaris to have both stdlib.h
and unistd.h
included in the one source file - here's a "hello world" that does just that.
drkirkby@hawk:~$ cat test.c #include <stdio.h> #include <unistd.h> #include <stdlib.h> int main() { printf("Hello world\n"); exit(0); } drkirkby@hawk:~$ gcc -Wall test.c drkirkby@hawk:~$ ./a.out Hello world
Changed 12 years ago by
Attachment: | trac-9221-matplotlib-update.patch added |
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comment:17 Changed 12 years ago by
With the patch, all doctests in plot/*.py pass with matplotlib 1.0.
comment:18 follow-up: 19 Changed 12 years ago by
Replying to drkirkby:
BTW, it perfectly possible on Solaris to have both
stdlib.h
andunistd.h
included in the one source file - here's a "hello world" that does just that.drkirkby@hawk:~$ cat test.c #include <stdio.h> #include <unistd.h> #include <stdlib.h> int main() { printf("Hello world\n"); exit(0); } drkirkby@hawk:~$ gcc -Wall test.c drkirkby@hawk:~$ ./a.out Hello world
Interesting. In this case, it seems like they want to include Python.h.
By default, which of _XPG4 or _XPG3 is defined in your compiler? From the code in stdlib.h, it looks like setting _XPG4, but undefining _XPG3, should work.
comment:19 Changed 12 years ago by
Replying to jason:
Replying to drkirkby:
BTW, it perfectly possible on Solaris to have both
stdlib.h
andunistd.h
included in the one source file - here's a "hello world" that does just that.drkirkby@hawk:~$ cat test.c #include <stdio.h> #include <unistd.h> #include <stdlib.h> int main() { printf("Hello world\n"); exit(0); } drkirkby@hawk:~$ gcc -Wall test.c drkirkby@hawk:~$ ./a.out Hello worldInteresting. In this case, it seems like they want to include Python.h.
I've no idea.
By default, which of _XPG4 or _XPG3 is defined in your compiler?
Neither of them.
One can see what gets defined with any combination of C and header files by pre-processing a file, and using the -dM options. To get the defaults, just use an empty file or /dev/null. This is a very useful trick some times.
drkirkby@laptop:~$ gcc -dM -E - </dev/null #define __DBL_MIN_EXP__ (-1021) #define __FLT_MIN__ 1.17549435e-38F #define __CHAR_BIT__ 8 #define __WCHAR_MAX__ 2147483647 #define __DBL_DENORM_MIN__ 4.9406564584124654e-324 #define __FLT_EVAL_METHOD__ 2 etc etc
For the case of a test file where both unistd.h and stdlib.h are defined, we see both _XOPEN_XPG3
and _XOPEN_XPG4
get defined, but not _XPG3
or _XPG4
.
drkirkby@laptop:~$ gcc -dM -E test.c | grep XPG #define _XOPEN_XPG3 #define _XOPEN_XPG4
From the code in stdlib.h, it looks like setting _XPG4, but undefining _XPG3, should work.
I don't think one should go defining _XPG3
and _XPG4
directly, but if one does do that, then one can induce the error depending on what you define and what header files you include. I leave it for you to prove that to yourself. (Try it on 't2.math')
I can suggest a few resources that might shed some light on it.
- http://www.opengroup.org/forums/
- gcc-help mailing list. (The mainly Linux crowd are bound to blame Sun, but worth asking anyway.)
- comp.unix.solaris newsgroup http://groups.google.com/group/comp.unix.solaris
- comp.lang.c newsgroup http://groups.google.co.uk/group/comp.lang.c
There's probably a few more. Sorry I don't know the answer, but I doubt it needs on to go around defining _XPG4
or similar.
Dave
comment:20 Changed 12 years ago by
I'm attaching the standards(1) man page from an OpenSolaris machine. This gives some information on this matter. I've also asked on the newsgroup solaris.unix.solaris about this issue.
comment:22 follow-up: 23 Changed 12 years ago by
Can I get an account on a Solaris box and instructions for reproducing this problem? This is getting hard to debug without access to the hardware.
comment:23 Changed 12 years ago by
Replying to jason:
Can I get an account on a Solaris box and instructions for reproducing this problem? This is getting hard to debug without access to the hardware.
Ask William - he can give you an account on t2.math, which is a Solaris 10 SPARC system.
Dave
comment:24 Changed 12 years ago by
I'm trying it out on t2 right now. I logged into t2, extracted {{{/usr/local/sage-4.5.1-Solaris_10_SPARC-sun4u-SunOS.tar.gz}} to /scratch/grout, and then tried (as a control) to install the current matplotlib spkg:
./sage -f spkg/standard/matplotlib-0.99.3.spkg
gave errors like these:
building 'matplotlib.ft2font' extension creating build/temp.solaris-2.10-sun4v-2.6 creating build/temp.solaris-2.10-sun4v-2.6/src creating build/temp.solaris-2.10-sun4v-2.6/CXX gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -I/scratch/grout/sage-4.5.1-Solaris_10_SPARC-sun4u-SunOS/local/lib/python2.6/site-packages/numpy/core/include -I/export/home/drkirkby/sage-4.5.1/local/include/freetype2 -I/export/home/drkirkby/sage-4.5.1/local/include -I/scratch/grout/sage-4.5.1-Solaris_10_SPARC-sun4u-SunOS/local/include/ -I/usr/local/include -I. -I/scratch/grout/sage-4.5.1-Solaris_10_SPARC-sun4u-SunOS/local/include/python2.6 -c src/ft2font.cpp -o build/temp.solaris-2.10-sun4v-2.6/src/ft2font.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from /usr/local/gcc-4.4.1-sun-linker/bin/../lib/gcc/sparc-sun-solaris2.10/4.4.1/../../../../include/c++/4.4.1/ext/hash_map:59, from ./CXX/Extensions.hxx:68, from src/ft2font.h:4, from src/ft2font.cpp:1: /usr/local/gcc-4.4.1-sun-linker/bin/../lib/gcc/sparc-sun-solaris2.10/4.4.1/../../../../include/c++/4.4.1/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. In file included from src/ft2font.h:13, from src/ft2font.cpp:1: /scratch/grout/sage-4.5.1-Solaris_10_SPARC-sun4u-SunOS/local/include/ft2build.h:56:38: error: freetype/config/ftheader.h: No such file or directory In file included from src/ft2font.cpp:1: src/ft2font.h:14:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:15:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:16:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:17:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:18:10: error: #include expects "FILENAME" or <FILENAME> In file included from src/ft2font.cpp:1: src/ft2font.h:31: error: ‘FT_Bitmap’ has not been declared src/ft2font.h:31: error: ‘FT_Int’ has not been declared src/ft2font.h:31: error: ‘FT_Int’ has not been declared src/ft2font.h:77: error: ISO C++ forbids declaration of ‘FT_Face’ with no type src/ft2font.h:77: error: expected ‘,’ or ‘...’ before ‘&’ token src/ft2font.h:83: error: ISO C++ forbids declaration of ‘FT_Face’ with no type src/ft2font.h:83: error: expected ‘,’ or ‘...’ before ‘&’ token src/ft2font.h:122: error: ‘FT_Face’ does not name a type src/ft2font.h:123: error: ‘FT_Matrix’ does not name a type src/ft2font.h:124: error: ‘FT_Vector’ does not name a type src/ft2font.h:125: error: ‘FT_Error’ does not name a type src/ft2font.h:126: error: ‘FT_Glyph’ was not declared in this scope src/ft2font.h:126: error: template argument 1 is invalid src/ft2font.h:126: error: template argument 2 is invalid src/ft2font.h:127: error: ‘FT_Vector’ was not declared in this scope src/ft2font.h:127: error: template argument 1 is invalid src/ft2font.h:127: error: template argument 2 is invalid src/ft2font.h:133: error: ‘FT_BBox’ does not name a type src/ft2font.cpp:45: error: ‘FT_Library’ does not name a type src/ft2font.cpp:96: error: variable or field ‘draw_bitmap’ declared void src/ft2font.cpp:96: error: ‘FT_Bitmap’ was not declared in this scope src/ft2font.cpp:96: error: ‘bitmap’ was not declared in this scope src/ft2font.cpp:97: error: ‘FT_Int’ was not declared in this scope src/ft2font.cpp:98: error: ‘FT_Int’ was not declared in this scope /scratch/grout/sage-4.5.1-Solaris_10_SPARC-sun4u-SunOS/local/lib/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: ‘int _import_array()’ defined but not used error: command 'gcc' failed with exit status 1 Error building matplotlib package.
Do you know how I can get up to at least installing the current matplotlib spkg on t2? When I tried my updated 1.0 spkg, I also got these errors.
comment:25 Changed 12 years ago by
FYI, I did do the recommended . /usr/local/gcc-4.4.1-sun-linker/gcc441sun
first.
comment:26 Changed 12 years ago by
It appears that the problem is in sage-location. Note that the local/lib/pkgconfig/freetype2.pc file is
prefix=/export/home/drkirkby/sage-4.5.1/local exec_prefix=${prefix} libdir=${exec_prefix}/lib includedir=${prefix}/include Name: FreeType 2 Description: A free, high-quality, and portable font engine. Version: 9.16.3 Requires: Libs: -L${libdir} -lfreetype -lz Cflags: -I${includedir}/freetype2 -I${includedir}
which means it points to totally the wrong place once Sage is moved. This should be fixed over on #9210.
comment:27 follow-up: 29 Changed 12 years ago by
Jason,
I have no idea why this did not work for you. That binary was not built on 't2' but on another machine, with the expectation it would work on any SPARC. However, I am aware moving Sage does not always work.
I can only suggest you build the latest Sage from source. Just remember to set something like
export SAGE_PARALLEL_SPKG_BUILD=yes export MAKE="make -j8"
otherwise it will take ages to build.
Dave
comment:28 Changed 12 years ago by
BTW, there's a binary at
/scratch/sage-4.5.3.rc0-binary.tar
you could try extracting that.
But again, it has been moved, though in that case the binary was built on t2.math.
Dave
comment:29 Changed 12 years ago by
Replying to drkirkby:
Jason,
I have no idea why this did not work for you. That binary was not built on 't2' but on another machine, with the expectation it would work on any SPARC. However, I am aware moving Sage does not always work.
I can only suggest you build the latest Sage from source. Just remember to set something like
export SAGE_PARALLEL_SPKG_BUILD=yes export MAKE="make -j8"otherwise it will take ages to build.
Thanks; I'll do that. I'm 99% sure my problem is caused by a Sage directory move.
comment:30 follow-up: 31 Changed 12 years ago by
Status: | needs_work → needs_review |
---|
Okay, I've updated the spkg so that it works on t2 (and passes all matplotlib tests):
http://sage.math.washington.edu/home/jason/matplotlib-1.0.0.spkg
Can people try it? Basically, I just deleted in CXX/WrapPython.h any fudging with the defines, based on drkirkby's idea above that it ought not have to do that. The new WrapPython?.h is:
#ifndef __PyCXX_wrap_python_hxx__ #define __PyCXX_wrap_python_hxx__ // On some platforms we have to include time.h to get select defined #if !defined(__WIN32__) && !defined(WIN32) && !defined(_WIN32) && !defined(_WIN64) #include <sys/time.h> #endif // pull in python definitions #include <Python.h> #endif
Here it passes the matplotlib test suite:
In [1]: import matplotlib In [2]: matplotlib.__version__ Out[2]: '1.0.0' In [3]: matplotlib.test() /scratch/grout/sage-4.5.3/local/lib/python2.6/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=730139.0, right=730139.0 + 'left=%s, right=%s') % (left, right)) ---------------------------------------------------------------------- Ran 138 tests in 755.419s OK (KNOWNFAIL=42) Out[3]: True
comment:31 follow-up: 33 Changed 12 years ago by
Replying to jason:
Okay, I've updated the spkg so that it works on t2 (and passes all matplotlib tests):
http://sage.math.washington.edu/home/jason/matplotlib-1.0.0.spkg
Can people try it?
I should be able to try this on OS X 10.4 PPC today or tomorrow.
comment:32 Changed 12 years ago by
Okay, I've composed a long message to matplotlib-devel about this issue:
http://sourceforge.net/mailarchive/message.php?msg_name=4C9262A9.5040901%40creativetrax.com
comment:33 follow-up: 37 Changed 12 years ago by
Replying to kcrisman:
Replying to jason:
Okay, I've updated the spkg so that it works on t2 (and passes all matplotlib tests):
http://sage.math.washington.edu/home/jason/matplotlib-1.0.0.spkg
Can people try it?
I should be able to try this on OS X 10.4 PPC today or tomorrow.
Seems to be working a-ok here, no issues.
By the way, to drkirkby, looks like matplotlib also uses nose
to run their tests, like scipy and numpy. I get no indication that SAGE_CHECK=yes
does anything - or would - because of that.
---------------------------------------------------------------------- | Sage Version 4.6.prealpha4, Release Date: 2010-09-07 | | Type notebook() for the GUI, and license() for information. | ---------------------------------------------------------------------- ********************************************************************** * * * Warning: this is a prerelease version, and it may be unstable. * * * ********************************************************************** sage: import mat math matplotlib sage: import matplotlib sage: matplotlib.test() --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /Users/student/<ipython console> in <module>() /Users/student/Desktop/sage-4.6.prealpha4/local/lib/python2.6/site-packages/matplotlib/__init__.pyc in test(verbosity) 922 def test(verbosity=0): 923 """run the matplotlib test suite""" --> 924 import nose 925 import nose.plugins.builtin 926 from testing.noseclasses import KnownFailure ImportError: No module named nose
If we want to test these automatically, we need nose; just adding the lines to spkg-check
or spkg-install
won't help. Obviously this is a different ticket, but I wanted to point it out. And I'd support adding this to Sage if it improved things overall.
comment:35 Changed 12 years ago by
Sorry; I should have CCd you on this: #9221
??? That's this ticket, which I'm obviously already cc:ed on. Did you mean something else related to nose?
comment:36 Changed 12 years ago by
Yes: #9921. Notice that it's convenient that related tickets have numbers so similar :).
comment:37 Changed 12 years ago by
Replying to kcrisman:
Replying to kcrisman:
Replying to jason:
Okay, I've updated the spkg so that it works on t2 (and passes all matplotlib tests):
http://sage.math.washington.edu/home/jason/matplotlib-1.0.0.spkg
Can people try it?
I should be able to try this on OS X 10.4 PPC today or tomorrow.
Seems to be working a-ok here, no issues.
By the way, to drkirkby, looks like matplotlib also uses
nose
to run their tests, like scipy and numpy. I get no indication thatSAGE_CHECK=yes
does anything - or would - because of that.
See
where only today I suggested we make 'nose' a standard package.
If we want to test these automatically, we need nose; just adding the lines to
spkg-check
orspkg-install
won't help. Obviously this is a different ticket, but I wanted to point it out. And I'd support adding this to Sage if it improved things overall.
As far as I can see, adding nose as a stranded package would be very low risk, as nothing would depend on it except during testing. So it can't hardly screw Sage up, as long as nose builds reliably itself. Even if it was totally non-functional, it would not hurt sage.
What we need is a list of packages that use nose, then request it is added as standard on the basis we can't test otherwise. It might be able to escape the 'experimental' stage.
Dave
comment:38 Changed 12 years ago by
Report Upstream: | Reported upstream. Developers acknowledge bug. → Fixed upstream, but not in a stable release. |
---|
Eric Firing just committed a fix to matplotlib SVN which takes care of these compiling issues on Solaris. Thanks for David for the tipoff on how to solve these issues (i.e., delete the kludgy defines).
See http://matplotlib.svn.sourceforge.net/viewvc/matplotlib?view=revision&revision=8707 for the commit log upstream.
comment:39 Changed 12 years ago by
(so in the next release, we can delete the patch I added to the spkg fixing the Solaris compiling issue).
comment:40 Changed 12 years ago by
Ping about a review---can anyone review this? The new spkg works on solaris (t2). The new version of matplotlib adds some very nice features and allows us to clean up the spkg quite a bit.
comment:41 follow-up: 42 Changed 12 years ago by
Another friendly ping to people to look at this ticket and review it...
comment:42 Changed 12 years ago by
Another friendly ping to people to look at this ticket and review it...
I'd love to, but there is too much technical shell stuff mentioned in the comments so I don't want to be responsible for breaking something somewhere.
comment:43 follow-up: 44 Changed 12 years ago by
As I see it, the only outstanding problem was that it didn't compile on Solaris. We fixed that (I compiled it on t2), but it doesn't seem appropriate for me to set the ticket to positive review. I was hoping for someone to give it one last try on their standard platform.
David, can you confirm that this spkg now works on Solaris? If not, kcrisman, can you just check that it works on your platform still?
comment:44 Changed 12 years ago by
Replying to jason:
As I see it, the only outstanding problem was that it didn't compile on Solaris. We fixed that (I compiled it on t2), but it doesn't seem appropriate for me to set the ticket to positive review. I was hoping for someone to give it one last try on their standard platform.
David, can you confirm that this spkg now works on Solaris? If not, kcrisman, can you just check that it works on your platform still?
Jason, that was the version I tried!
Seems to be working fine on OS X 10.6 right now, tested the live documentation and the output at various spots. Currently running doctests.
comment:45 Changed 12 years ago by
Reviewers: | → David Kirkby, Karl-Dieter Crisman |
---|---|
Status: | needs_review → positive_review |
Okay, all is well. I love some of those plot doc graphics! One definitely also needs the patch for the axis labels to look right - interesting change in API, though of course it was a switch from 0.x to 1.y!
As long as you are confident enough that t2 working is good (and indeed, drkirkby didn't say boo although he commented after that) then I'll set to positive review.
comment:46 Changed 12 years ago by
comment:47 Changed 12 years ago by
Merged in: | → sage-4.6.alpha2 |
---|---|
Resolution: | → fixed |
Status: | positive_review → closed |
comment:48 Changed 12 years ago by
Has anyone tested the new package with a full build of Sage from scratch? I'm getting very many doctest errors that appears to stem from missing .ttf files. I'll investigate further.
comment:49 Changed 12 years ago by
I haven't tested that configuration. Can you post some of these errors here?
comment:50 follow-up: 58 Changed 12 years ago by
I made a source distribution from 4.6.alpha1 + #9221 and built it in a directory named sage-4.6.alpha2-9221
. The long doctests pass. I moved the directory to a different place.
I made a source distribution from the latest trial 4.6.alpha2 + #9221 and built it in a directory named sage-4.6.alpha2pre2
, i.e., it's different from the previous build directory. Many tests fail with
RuntimeError: Could not open facefile /mnt/usb1/scratch/mpatel/tmp/sage-4.6.alpha2-9221/local/lib/python/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource
The full log is here. I think the problem is that
$ grep 9221 $HOME/.matplotlib/fontList.cache | grep Vera.ttf S'/mnt/usb1/scratch/mpatel/tmp/sage-4.6.alpha2-9221/local/lib/python/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf' aS'/mnt/usb1/scratch/mpatel/tmp/sage-4.6.alpha2-9221/local/lib/python/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf' $ grep 9221 $HOME/.matplotlib/fontList.cache | wc 128 128 16666
comment:51 Changed 12 years ago by
Status: | closed → needs_work |
---|
After moving $HOME/.matplotlib
to a different place, I've rerun the tests in sage-4.6.alpha2pre2
. I see many failures with
AttributeError: 'module' object has no attribute 'cbook'
See this log. (I stopped the tests early.)
I've started the tests again and now they appear to be passing.
comment:52 Changed 12 years ago by
Status: | needs_work → needs_info |
---|
comment:53 Changed 12 years ago by
Merged in: | sage-4.6.alpha2 |
---|---|
Status: | needs_info → needs_work |
I'm removing this from 4.6.alpha2, but there's still time for it in alpha3.
comment:54 Changed 12 years ago by
If you still have the directories around, keep the .matplotlib directory, but delete the fontList.cache file (it's a cache that should be automagically regenerated).
comment:55 Changed 12 years ago by
Relevant docs: http://matplotlib.sourceforge.net/faq/troubleshooting_faq.html#matplotlib-directory-location
Maybe Sage should set the MPLCONFIGDIR to point to something inside the Sage tree.
comment:57 Changed 12 years ago by
Status: | needs_work → needs_info |
---|
When I move things around to try to duplicate the issue, the cache file is automatically updated after plotting something using fonts. So I'll try to recreate your problem with a fresh source+9221 build.
comment:58 Changed 12 years ago by
Replying to mpatel:
I made a source distribution from 4.6.alpha1 + #9221 and built it in a directory named
sage-4.6.alpha2-9221
. The long doctests pass. I moved the directory to a different place.I made a source distribution from the latest trial 4.6.alpha2 + #9221 and built it in a directory named
sage-4.6.alpha2pre2
, i.e., it's different from the previous build directory. Many tests fail with
I assume this is on sage.math? Can you make the latest trial 4.6.alpha2 tarball available somewhere so I can try to reproduce what you did?
comment:59 Changed 12 years ago by
I built on sage.math. The latest trial 4.6.alpha2, which is likely final, as the builds appear to be going well, is in http://sage.math.washington.edu/home/release/sage-4.6.alpha2/ .
comment:60 follow-up: 61 Changed 12 years ago by
I'm going to try to reproduce this first on sage.math. Do I just replace the matplotlib-0.99.3 spkg with my spkg in the source tarball, then build? Is there something more I need to do?
comment:61 Changed 12 years ago by
Replying to jason:
I'm going to try to reproduce this first on sage.math. Do I just replace the matplotlib-0.99.3 spkg with my spkg in the source tarball, then build? Is there something more I need to do?
That should work. The colormap tests fixed by the patch will fail, but if the errors I saw show up --- i.e., they're not part of the "fog of merge" --- they'll be easy to distinguish.
comment:62 Changed 12 years ago by
I've reproduced the problem and emailed the matplotlib mailing list. I'll also try tracking this down a bit this afternoon.
comment:63 Changed 12 years ago by
The reply on matplotlib-users is that this is already fixed in SVN. I'll get the commit, apply the patch, and update the spkg.
comment:64 follow-up: 65 Changed 12 years ago by
Status: | needs_info → needs_review |
---|
Okay, I've updated the spkg (at the original address in the description) with the patch from matplotlib SVN that should take care of the problem. I'm building this momentarily.
I'm putting this as needs review so that one or two others can double-check this. kcrisman?
comment:65 Changed 12 years ago by
I'm putting this as needs review so that one or two others can double-check this. kcrisman?
I'll do my best, but might not be able to test it on something you don't have access to already (you have OS X 10.6, and access to sage.math) until after the weekend.
comment:66 Changed 12 years ago by
I can at least confirm that this mpl package installs fine with ./sage -i
on a relatively new (but not brand new) build of 4.6.alpha1. I hope that is helpful; I don't have time to run any tests on this machine now.
comment:67 Changed 12 years ago by
mpatel: I just built a fresh copy of 4.6.alpha2 on sage.math with the new spkg (linked above) and ran ptestlong. I got the two colormap failures that are solved in the patch on this ticket, as well as two other failures that seem totally unrelated to this spkg.
So I think we are good to go. I feel weird setting this back to positive review, but can you try merging it again and "reviewing" the change to make sure it fixes the error you were seeing?
comment:68 Changed 12 years ago by
I haven't looked at the code at all, but it builds and passes tests for me on an Intel Mac OS X 10.6 box, skynet machine taurus (linux: x86_64-Linux-nehalem-fc), and skynet machine fulvia (Solaris on x86: x86_64-SunOS-core2). I also deleted my .matplotlib directory and reran the tests on taurus, and they passed again. I haven't been following this ticket; is this good enough to restore the positive review?
comment:70 Changed 12 years ago by
Status: | needs_review → positive_review |
---|
comment:71 Changed 12 years ago by
There are uncommitted changes
matplotlib-1.0.0$ hg stat ? patches/WrapPython.h ? patches/WrapPython.h.diff
By the way, is this the patch that fixes the font cache problem?
comment:72 Changed 12 years ago by
Status: | positive_review → needs_work |
---|
No, that's the previous version of the spkg. Apparently somehow the new version was not copied to my home directory on sage.math.
The new version is md5 28179fff25e33fc623f1de96a039eecc
I've just double-checked, and it is now the version in my home directory:
http://sage.math.washington.edu/home/jason/matplotlib-1.0.0.spkg
Sorry for the mess-up! I'm setting it back to needs_review, since apparently people reviewed the old spkg. mpatel---I think you building on sage.math would be sufficient to review this.
comment:73 Changed 12 years ago by
Status: | needs_work → needs_review |
---|
comment:74 follow-up: 79 Changed 12 years ago by
BTW, WrapPython?.h fixes the Solaris problem, and the font_manager.py patch fixes the font cache problem.
comment:75 Changed 12 years ago by
I wonder if maybe this happened because of the system maintenance on the home directory??? I don't know. I might have also made a mistake when I thought I copied the new spkg over.
comment:76 Changed 12 years ago by
Status: | needs_review → positive_review |
---|
comment:77 Changed 12 years ago by
Merged in: | → sage-4.6.alpha3 |
---|---|
Status: | positive_review → closed |
comment:78 Changed 12 years ago by
Thanks, Jason! The fontList.cache
is now quietly regenerated and the tests pass on sage.math.
comment:79 follow-up: 80 Changed 12 years ago by
Replying to jason:
BTW, WrapPython?.h fixes the Solaris problem, and the font_manager.py patch fixes the font cache problem.
Aren't these worth an spkg patch level? This also avoids confusion with previous versions.
comment:80 follow-up: 81 Changed 12 years ago by
Replying to leif:
Replying to jason:
BTW, WrapPython?.h fixes the Solaris problem, and the font_manager.py patch fixes the font cache problem.
Aren't these worth an spkg patch level? This also avoids confusion with previous versions.
I viewed this as part of the 1.0.0 spkg (these patches were necessary for the 1.0.0 spkg to be accepted and used).
comment:81 Changed 12 years ago by
Replying to jason:
Replying to leif:
Replying to jason:
BTW, WrapPython?.h fixes the Solaris problem, and the font_manager.py patch fixes the font cache problem.
Aren't these worth an spkg patch level? This also avoids confusion with previous versions.
I viewed this as part of the 1.0.0 spkg (these patches were necessary for the 1.0.0 spkg to be accepted and used).
:-) IMHO every spkg that's not almost vanilla upstream should carry a patch level, since the (Sage) package version (without the patch level) is not a Sage but the upstream version, but this appears to be an endless discussion...
comment:82 follow-up: 83 Changed 12 years ago by
I'm not the release manager, but IMHO either this ticket needs work, or #6235 / #9210? should be blockers for Sage 4.6, since
- installing Sage 4.6.alpha3 / matplotlib 1.0.0 breaks other Sage installations (cf. doctest errors in
sage/plot/plot.py
below, which even occur after rebuilding e.g. Sage 4.5.3 from scratch), - the current spkg / alpha3 again breaks upgrading (cf. #9896) if the original Sage installation has been moved (copied / renamed), which apparently is common user practice.
Unless one e.g. deletes $HOME/.matplotlib/
, the following happens with other Sage installations (and perhaps other software):
sage -t -long "devel/sage/sage/plot/plot.py" ********************************************************************** File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/devel/sage/sage/plot/plot.py", line 210: sage: P # show the result Exception raised: Traceback (most recent call last): File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_0[55]>", line 1, in <module> P # show the result###line 210: sage: P # show the result File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/sage/misc/displayhook.py", line 174, in displayhook print_obj(sys.stdout, obj) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/sage/misc/displayhook.py", line 142, in print_obj print >>out_stream, `obj` File "sage_object.pyx", line 101, in sage.structure.sage_object.SageObject.__repr__ (sage/structure/sage_object.c:1370) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/sage/plot/plot.py", line 915, in _repr_ self.show() File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/sage/plot/plot.py", line 1437, in show self.save(DOCTEST_MODE_FILE, **options) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/sage/plot/plot.py", line 1973, in save figure.savefig(filename,dpi=dpi,bbox_inches='tight',**options) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/figure.py", line 1032, in savefig self.canvas.print_figure(*args, **kwargs) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/backend_bases.py", line 1455, in print_figure **kwargs) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/backends/backend_agg.py", line 358, in print_png FigureCanvasAgg.draw(self) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/backends/backend_agg.py", line 314, in draw self.figure.draw(self.renderer) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/artist.py", line 46, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/figure.py", line 773, in draw for a in self.axes: a.draw(renderer) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/artist.py", line 46, in draw_wrapper draw(artist, renderer, *args, **kwargs) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/axes.py", line 1735, in draw a.draw(renderer) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/text.py", line 518, in draw bbox, info = self._get_layout(renderer) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/text.py", line 280, in _get_layout clean_line, self._fontproperties, ismath=ismath) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/backends/backend_agg.py", line 156, in get_text_width_height_descent self.mathtext_parser.parse(s, self.dpi, prop) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/mathtext.py", line 2797, in parse font_output = fontset_class(prop, backend) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/mathtext.py", line 658, in __init__ self._stix_fallback = StixFonts(*args, **kwargs) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/mathtext.py", line 900, in __init__ fullpath = findfont(name) File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python/site-packages/matplotlib/font_manager.py", line 1306, in findfont if not os.path.exists(font): File "/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/lib/python2.6/genericpath.py", line 18, in exists st = os.stat(path) TypeError: coercing to Unicode: need string or buffer, dict found ********************************************************************** ... [same exception in other examples] ... ********************************************************************** 5 items had failures: 1 of 71 in __main__.example_0 1 of 7 in __main__.example_13 1 of 8 in __main__.example_14 1 of 45 in __main__.example_30 1 of 89 in __main__.example_43 ***Test Failed*** 5 failures. For whitespace errors, see the file /home/leif/.sage//tmp/.doctest_plot.py
When trying to upgrade to 4.6.alpha3 in a renamed directory, installing matplotlib 1.0.0 fails with
... running build_ext building 'matplotlib.ft2font' extension creating build/temp.linux-x86_64-2.6 creating build/temp.linux-x86_64-2.6/src creating build/temp.linux-x86_64-2.6/CXX gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -march=native -O3 -fno-strict-aliasing -fomit-frame-pointer -DHONORS_CFLAGS -march=native -O3 -DHONORS_CPPFLAGS -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/lib/python2.6/site-packages/numpy/core/include -I/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/include/freetype2 -I/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-to-rename/local/include -I/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/include -I. -I/home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/include/python2.6 -c src/ft2font.cpp -o build/temp.linux-x86_64-2.6/src/ft2font.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from /home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/include/python2.6/Python.h:8, from ./CXX/WrapPython.h:47, from ./CXX/Extensions.hxx:37, from src/ft2font.h:4, from src/ft2font.cpp:1: /home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/include/python2.6/pyconfig.h:1028:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/sys/time.h:23, from ./CXX/WrapPython.h:43, from ./CXX/Extensions.hxx:37, from src/ft2font.h:4, from src/ft2font.cpp:1: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/include/python2.6/Python.h:8, from ./CXX/WrapPython.h:47, from ./CXX/Extensions.hxx:37, from src/ft2font.h:4, from src/ft2font.cpp:1: /home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/include/python2.6/pyconfig.h:1037:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/sys/time.h:23, from ./CXX/WrapPython.h:43, from ./CXX/Extensions.hxx:37, from src/ft2font.h:4, from src/ft2font.cpp:1: /usr/include/features.h:160:1: warning: this is the location of the previous definition In file included from src/ft2font.h:14, from src/ft2font.cpp:1: /home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/include/ft2build.h:56:38: error: freetype/config/ftheader.h: No such file or directory In file included from src/ft2font.cpp:1: src/ft2font.h:15:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:16:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:17:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:18:10: error: #include expects "FILENAME" or <FILENAME> src/ft2font.h:19:10: error: #include expects "FILENAME" or <FILENAME> In file included from src/ft2font.cpp:1: src/ft2font.h:33: error: 'FT_Bitmap' has not been declared src/ft2font.h:33: error: 'FT_Int' has not been declared src/ft2font.h:33: error: 'FT_Int' has not been declared src/ft2font.h:89: error: ISO C++ forbids declaration of 'FT_Face' with no type src/ft2font.h:89: error: expected ',' or '...' before '&' token src/ft2font.h:95: error: ISO C++ forbids declaration of 'FT_Face' with no type src/ft2font.h:95: error: expected ',' or '...' before '&' token src/ft2font.h:137: error: 'FT_Face' does not name a type src/ft2font.h:138: error: 'FT_Matrix' does not name a type src/ft2font.h:139: error: 'FT_Vector' does not name a type src/ft2font.h:140: error: 'FT_Error' does not name a type src/ft2font.h:141: error: 'FT_Glyph' was not declared in this scope src/ft2font.h:141: error: template argument 1 is invalid src/ft2font.h:141: error: template argument 2 is invalid src/ft2font.h:142: error: 'FT_Vector' was not declared in this scope src/ft2font.h:142: error: template argument 1 is invalid src/ft2font.h:142: error: template argument 2 is invalid src/ft2font.h:148: error: 'FT_BBox' does not name a type src/ft2font.cpp:45: error: 'FT_Library' does not name a type src/ft2font.cpp:108: error: variable or field 'draw_bitmap' declared void src/ft2font.cpp:108: error: 'FT_Bitmap' was not declared in this scope src/ft2font.cpp:108: error: 'bitmap' was not declared in this scope src/ft2font.cpp:109: error: 'FT_Int' was not declared in this scope src/ft2font.cpp:110: error: 'FT_Int' was not declared in this scope /home/leif/Sage/sage-4.5.3-for-4.6.alpha3-renamed/local/lib/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: 'int _import_array()' defined but not used error: command 'gcc' failed with exit status 1 Error building matplotlib package.
comment:83 follow-up: 84 Changed 12 years ago by
Replying to leif:
I'm not the release manager, but IMHO either this ticket needs work, or #6235 / #9210? should be blockers for Sage 4.6, since
- installing Sage 4.6.alpha3 / matplotlib 1.0.0 breaks other Sage installations (cf. doctest errors in
sage/plot/plot.py
below, which even occur after rebuilding e.g. Sage 4.5.3 from scratch),
Are you sure that you have the most recent (i.e., the merged) 1.0.0 spkg from this ticket? Can you try sage -f just in case (you see that there have been updates to the 1.0.0 spkg on this ticket as time went on)
Or wait. Are you saying that the font cache file created by the new(est) spkg here is causing problems with older versions of matplotlib?
comment:84 Changed 12 years ago by
Replying to jason:
Replying to leif:
I'm not the release manager, but IMHO either this ticket needs work, or #6235 / #9210? should be blockers for Sage 4.6, since
- installing Sage 4.6.alpha3 / matplotlib 1.0.0 breaks other Sage installations (cf. doctest errors in
sage/plot/plot.py
below, which even occur after rebuilding e.g. Sage 4.5.3 from scratch),Are you sure that you have the most recent (i.e., the merged) 1.0.0 spkg from this ticket? Can you try sage -f just in case (you see that there have been updates to the 1.0.0 spkg on this ticket as time went on)
I only have the current 1.0.0 one, but that doesn't solve the problems older MPL installations have. ;-)
Or wait. Are you saying that the font cache file created by the new(est) spkg here is causing problems with older versions of matplotlib?
Exactly that. It seems they've changed the format s.t. older MPL versions expecting an older format (without doing any consistency / type / error checking) pass a dictionary to os.path.exists()
.
comment:85 follow-ups: 86 88 Changed 12 years ago by
comment:86 follow-ups: 87 91 Changed 12 years ago by
Replying to mpatel:
Leif, do the current patches at #6235 and #9210 fix the problems you've found?
I'm pretty sure #6235 fixes (at least Sage's) MPL 1.0.0 breaking older installations.
Modifying $SAGE_ROOT/local/lib/pkgconfig/freetype2.pc
on Sage relocations perhaps fixes later build errors (including upgrades) of dependent packages like MPL; I haven't looked at nor tested the patch though. (Forcing reinstallation of freetype after moving Sage fixes it; but that's of course just a work-around, cf. #9896.)
At least for freetype, it should be possible to simply set prefix
to $SAGE_LOCAL
(unexpanded) rather than a hard-coded absolute path. (Done once, e.g. in its spkg-install
.)
comment:87 Changed 12 years ago by
Replying to leif:
At least for freetype, it should be possible to simply set
prefix
to$SAGE_LOCAL
(unexpanded) rather than a hard-coded absolute path. (Done once, e.g. in itsspkg-install
.)
prefix=${SAGE_LOCAL} exec_prefix=${prefix} libdir=${exec_prefix}/lib includedir=${prefix}/include Name: FreeType 2 Description: A free, high-quality, and portable font engine. Version: 9.16.3 Requires: Libs: -L${libdir} -lfreetype Cflags: -I${includedir}/freetype2 -I${includedir}
works for me. (The curly braces are mandatory.)
comment:88 follow-up: 89 Changed 12 years ago by
Replying to mpatel:
Leif, do the current patches at #6235 and #9210 fix the problems you've found?
Obviously #9210 doesn't help with upgrades from older versions, i.e. upgrading to 4.6. So for 4.6, it's perhaps better to fix the freetype spkg (though even preparing a fake new spkg would suffice for the moment).
Again hard-coding SAGE_ROOT
into the .pc
files is IMHO superfluous btw.
comment:89 follow-up: 90 Changed 12 years ago by
Replying to leif:
Replying to mpatel:
Leif, do the current patches at #6235 and #9210 fix the problems you've found?
Obviously #9210 doesn't help with upgrades from older versions, i.e. upgrading to 4.6. So for 4.6, it's perhaps better to fix the freetype spkg (though even preparing a fake new spkg would suffice for the moment).
For 4.6, I suggest we just bump up the patch level for freetype. Could you do this and add a link to the new spkg here?
comment:90 Changed 12 years ago by
Replying to mpatel:
Replying to leif:
Replying to mpatel:
Leif, do the current patches at #6235 and #9210 fix the problems you've found?
Obviously #9210 doesn't help with upgrades from older versions, i.e. upgrading to 4.6. So for 4.6, it's perhaps better to fix the freetype spkg (though even preparing a fake new spkg would suffice for the moment).
For 4.6, I suggest we just bump up the patch level for freetype. Could you do this and add a link to the new spkg here?
I've put an "updated" spkg at
http://sage.math.washington.edu/home/mpatel/trac/9221/freetype-2.3.5.p3.spkg
comment:91 follow-up: 92 Changed 12 years ago by
Replying to leif:
At least for freetype, it should be possible to simply set
prefix
to$SAGE_LOCAL
(unexpanded) rather than a hard-coded absolute path. (Done once, e.g. in itsspkg-install
.)
That's fantastic! It sounds like we should investigate doing that for the other packages as well (like libpng, etc.) There are some places in the pkgconfig files where the path is used in places other than the prefix, so doing this trick may not solve everything, but probably would solve a lot of the issues with pkgconfig files.
comment:92 Changed 12 years ago by
Replying to jason:
Replying to leif:
At least for freetype, it should be possible to simply set
prefix
to$SAGE_LOCAL
(unexpanded) rather than a hard-coded absolute path. (Done once, e.g. in itsspkg-install
.)That's fantastic! It sounds like we should investigate doing that for the other packages as well (like libpng, etc.) There are some places in the pkgconfig files where the path is used in places other than the prefix, so doing this trick may not solve everything, but probably would solve a lot of the issues with pkgconfig files.
I've made this idea #10202. Leif, do you think we can do this at compile time, or do we have to fix up the pkgconfig file after the spkg is installed? I'm guessing the latter.
The SVN spkg does not compile on Solaris. See the issues with header files reported at the end of #9202.