Seaborn in sage

[Laurent Decreusefond]

I recently discovered Seaborn, which is a visualization library on top
of matplotlib. It doesn't seem to be included in sage 7.2. Is there any
projet to do so ? or is there something equivalent ?

Best,

[Andrey Novoseltsev]

While it is not included, you can install it yourself via pip (SageMathCell does it):

sage -pip install seaborn

[Laurent Decreusefond]

Thanks. I tried to do it in the command line on a fresh install of Sage 7.2 and I got this error message (the full log is attached) :

[snip]

    In file included from /Users/Laurent/Downloads/sage-7.2/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-macosx-10.9-x86_64.egg/numpy/core/include/numpy/ndarraytypes.h:1777:0,

                     from /Users/Laurent/Downloads/sage-7.2/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-macosx-10.9-x86_64.egg/numpy/core/include/numpy/ndarrayobject.h:18,

                     from /Users/Laurent/Downloads/sage-7.2/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-macosx-10.9-x86_64.egg/numpy/core/include/numpy/arrayobject.h:4,

                     from pandas/src/datetime/np_datetime.c:18:

    /Users/Laurent/Downloads/sage-7.2/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-macosx-10.9-x86_64.egg/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

     #warning "Using deprecated NumPy API, disable it by " \

      ^

    /var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:984:suffix or operands invalid for `movq'

    /var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:2605:suffix or operands invalid for `movq'

    /var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:4735:suffix or operands invalid for `movq'

    error: command 'gcc' failed with exit status 1

[Dima Pasechnik]

errors like you get:

/var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:984:suffix or operands invalid for `movq'

indicate that your Sage's compiler toolchain is broken in some way, probably incompatible with your hardware.

A way to fix this would be to build Sage from source.

[Nathan Dunfield]

On Wednesday, July 27, 2016 at 3:30:47 AM UTC-5, Dima Pasechnik wrote:

errors like you get:

/var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:984:suffix or operands invalid for `movq'

indicate that your Sage's compiler toolchain is broken in some way, probably incompatible with your hardware.

A way to fix this would be to build Sage from source.

I believe this issue is likely the same as:

https://trac.sagemath.org/ticket/20563

As Dima says, building all of Sage from source will fix this.  An quicker solution might be to make sure you installed the version of Sage from 

http://mirrors.mit.edu/sage/osx/intel/index.html

whose label matches your version of OS X.  

Best,

Nathan

[leif]

Dima Pasechnik wrote:
> errors like you get:
>
>
> /var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:984:suffix or operands invalid for `movq'
>
>
> indicate that your Sage's compiler toolchain is broken in some way,
> probably incompatible with your hardware.
> A way to fix this would be to build Sage from source.

Nope, it's Apple's dead old version of the GNU assembler.

(Newer Xcode versions by default use the one from LLVM, but require
newer versions of MacOS X as well.)

If one passes '-q' to the assembler, clang's/LLVM's will get used
instead, so you could try adding '-Wa,-q' to CFLAGS and CXXFLAGS in
order to let GCC pass '-q' to the assembler, by doing for example

$ env CFLAGS="-Wa,-q" CXXFLAGS="-Wa,-q" ./sage -i <package>


Another way is to create a wrapper script $SAGE_LOCAL/bin/as which calls
the assembler with '-q' added to the options; see the following trac
tickets for more details:

https://trac.sagemath.org/ticket/20779

https://trac.sagemath.org/ticket/20563 (same issue, i.e. with movq)

(Both a bit stalled at the moment, but give more info on the general
problem with Xcode versions < 7.0.)


-leif

[leif]

Nathan Dunfield wrote:
> On Wednesday, July 27, 2016 at 3:30:47 AM UTC-5, Dima Pasechnik wrote:
>
> errors like you get:
>
>
> /var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:984:suffix or operands invalid for `movq'
>
>
> indicate that your Sage's compiler toolchain is broken in some way,
> probably incompatible with your hardware.
> A way to fix this would be to build Sage from source.
>
>
> I believe this issue is likely the same as:
>
> https://trac.sagemath.org/ticket/20563
>
> As Dima says, building all of Sage from source will fix this.

Ok, I didn't get he was using a binary distribution of Sage.

Building from source (or perhaps just reinstalling the GCC package by
typing 'make gcc') should work /in this case/, but doing so only fixes
the problem with movd vs. movq.

(The suggestion in my other reply should still work as well, I think.)


> A quicker solution might be to make sure you installed the version of Sage

> from
>
> http://mirrors.mit.edu/sage/osx/intel/index.html
>
> whose label matches your version of OS X.

Yep, there meanwhile is one specifically for MacOS X 10.9.


-leif

[Laurent Decreusefond]

I will try this one since I'm already working on a fresh, compiled from source, version of Sage.

[Laurent Decreusefond]

Thanks to your remarks, I realized that I had an old beta-version of Xcode (7.1) which was in conflict with the actual version (7.3.1). I relaunched the install with the correct version of Xcode and everything went smoothly. Thanks for your answers. 

[leif]

Laurent Decreusefond wrote:
> I will try this one since I'm already working on a fresh, compiled from
> source, version of Sage.

If you have Sage's GCC built on *your* system, the issue with movq will
disappear (since GCC checks exactly that feature of the assembler at its
*build* time).

But you /may/ run into similar problems ("No such instruction: ...")
when for example building NTL, since Apple's old GAS doesn't support
AVX, BMI etc. Then you can try what I suggested, or see #20779 (and
#21064 especially for NTL).


-leif

> Le mercredi 27 juillet 2016 19:45:55 UTC+2, leif a écrit :
>
> Dima Pasechnik wrote:
> > errors like you get:
> >
> >
> >
> /var/folders/md/71gv03bs6mx4qxg933r_k_x40000gn/T//ccSLsnmg.s:984:suffix
> or operands invalid for `movq'
> >
> >
> > indicate that your Sage's compiler toolchain is broken in some way,
> > probably incompatible with your hardware.
> > A way to fix this would be to build Sage from source.
>
> Nope, it's Apple's dead old version of the GNU assembler.
>
> (Newer Xcode versions by default use the one from LLVM, but require
> newer versions of MacOS X as well.)
>
> If one passes '-q' to the assembler, clang's/LLVM's will get used
> instead, so you could try adding '-Wa,-q' to CFLAGS and CXXFLAGS in
> order to let GCC pass '-q' to the assembler, by doing for example
>
> $ env CFLAGS="-Wa,-q" CXXFLAGS="-Wa,-q" ./sage -i <package>
>
>
> Another way is to create a wrapper script $SAGE_LOCAL/bin/as which
> calls
> the assembler with '-q' added to the options; see the following trac
> tickets for more details:
>
> https://trac.sagemath.org/ticket/20779

> <https://trac.sagemath.org/ticket/20779>
>
> https://trac.sagemath.org/ticket/20563

[leif]

Laurent Decreusefond wrote:
> Thanks to your remarks, I realized that I had an old beta-version of
> Xcode (7.1) which was in conflict with the actual version (7.3.1). I
> relaunched the install with the correct version of Xcode and everything
> went smoothly. Thanks for your answers.

Oh, interesting. (I thought you were running MacOS X 10.9.)

Which version actually is it? Yosemite (10.10) or already El Capitan
(10.11)?


-leif

> <https://trac.sagemath.org/ticket/20779>
>
> https://trac.sagemath.org/ticket/20563

[Laurent Decreusefond]

My version is on El Capitan 10.11.6