Scipy not compiling on Mac OS X

[Matthias Goerner]

I have Mac OS X 10.13 and I just downloaded the sage math 8.8 app dmg for Mac OS X 10.11 and 10.14 and tried to install ssl by running

/Applications/SageMath-8.8.app/sage -i openssl

/Applications/SageMath-8.8.app/sage -f python2

In both cases (the dmg for Mac OS X 10.11 and 10.14), the latter command fails at scipy when linking with gfortran saying:

    ld: library not found for -lSystem

    collect2: error: ld returned 1 exit status

What is going on?

[Dima Pasechnik]

libSystem.dylib is needed by libgfortran.dylib

Do you have /usr/lib/libSystem.dylib present?
Maybe it needs a different version of it.

Using a binary installation of Sage on a different OS version to
compile C/C++/Fortran
programs might be, hmm, tricky.
Build from source.

Or use conda, which, I think, does binary versions properly...



>
> --
> You received this message because you are subscribed to the Google Groups "sage-devel" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/e24a0b71-3e59-47cf-8f2f-14207e0b0d84%40googlegroups.com.

[Dima Pasechnik]

On Tue, Sep 17, 2019 at 9:31 AM Dima Pasechnik <dim...@gmail.com> wrote:
>
> On Tue, Sep 17, 2019 at 5:23 AM Matthias Goerner <enis...@gmail.com> wrote:
> >
> > I have Mac OS X 10.13 and I just downloaded the sage math 8.8 app dmg for Mac OS X 10.11 and 10.14 and tried to install ssl by running
> > /Applications/SageMath-8.8.app/sage -i openssl
> > /Applications/SageMath-8.8.app/sage -f python2
> >
> > In both cases (the dmg for Mac OS X 10.11 and 10.14), the latter command fails at scipy when linking with gfortran saying:
> > ld: library not found for -lSystem
> > collect2: error: ld returned 1 exit status
> >
> > What is going on?
>
> libSystem.dylib is needed by libgfortran.dylib
>
> Do you have /usr/lib/libSystem.dylib present?
> Maybe it needs a different version of it.

(i.e. libgfortran needs a particular version of libSystem - sorry for
sloppy writing)

>
> Using a binary installation of Sage on a different OS version to
> compile C/C++/Fortran
> programs might be, hmm, tricky.
> Build from source.
>
> Or use conda, which, I think, does binary versions properly...

one extra advantage of conda is that also building from source in
conda environment
is quick, as you can get most, if not all, unvendored libraries and
programs listed in
https://trac.sagemath.org/ticket/27330
from it.
(Same, to less extent, applies to Homebrew, by the way - they have fewer
than conda "system" package to use, though)

[Matthias Goerner]

So, I tried compiling from scratch and that failed as well - though with a different error (see other thread).

> > To unsubscribe from this group and stop receiving emails from it, send an email to sage-...@googlegroups.com.

[Matthias Koeppe]

This is probably the same as https://github.com/sagemath/binary-pkg/issues/19