Issues installing the optional "libhomfly" package

86 views
Skip to first unread message

Jesse H

unread,
Oct 10, 2017, 2:03:18 PM10/10/17
to sage-devel
Greetings,

I have been trying to use the function "homfly_polynomial()" from the Link package in Sage, but it requires an optional package "libhomfly": http://files.sagemath.org/spkg/upstream/libhomfly/index.html.

Unfortunately, when I try to install libhomfly ("sage -i libhomfly") the build always fails (see attached log file).

One of the dependencies for libhomfly is Boehm GC, but when I try to install this package ("sage -i boehm_gc"), it is not even found on Sage's list of optional packages (even though it's displayed on the website:http://mirrors-usa.go-parts.com/sage/sagemath/spkg/upstream/boehm_gc/index.html). I'm not sure if this is indeed the issue, but it's just something I came across.

For what it's worth, I'm running SageMath 8.0 and MacOS 10.12.6 on a mid 2012 MacBook Pro with a 2.3 GHz i7 processor and 8GB RAM.

Any help is much appreciated.

JH
libhomfly-1.0r2.log

Dima Pasechnik

unread,
Oct 10, 2017, 2:31:10 PM10/10/17
to sage-devel
to install Boehm GC Sage package, do

sage -i gc

Dima Pasechnik

unread,
Oct 10, 2017, 2:54:32 PM10/10/17
to sage-devel
although the linking error you got seems to be not related to GC.

Erik Bray

unread,
Oct 11, 2017, 5:18:45 AM10/11/17
to sage-devel
On Tue, Oct 10, 2017 at 8:31 PM, Dima Pasechnik <dim...@gmail.com> wrote:
> to install Boehm GC Sage package, do
>
> sage -i gc

gc is a standard package (dependency of ecl) so it would already be installed.

Erik Bray

unread,
Oct 11, 2017, 5:31:16 AM10/11/17
to sage-devel
This looks like a bug in libhomfly. Just looking at the sources it
has some messy handling of extern variable declarations vs.
definitions, and many global variables are actually being defined in
multiple modules. I haven't run into this problem myself building
libhomfly but maybe my compiler is more forgiving. Regardless it
definitely looks wrong to me. I could see if I can reproduce on OSX
now that I have shiny new access to a big OSX machine :)

Erik

Dima Pasechnik

unread,
Oct 11, 2017, 6:27:07 PM10/11/17
to sage-devel
I can reproduce this linking error on OSX; I've opened #24015 to track this error.

Dima Pasechnik

unread,
Oct 12, 2017, 5:29:46 AM10/12/17
to sage-devel
Now it's down to doing something with fmemopen call there, that is not portable to OSX (there is no fmemopen on OSX!)

How did this package get into Sage, it surely never ever worked on OSX...

Dima Pasechnik

unread,
Oct 13, 2017, 1:41:21 PM10/13/17
to sage-devel
It's fixed for OSX now, it's the packaging (and the necessary for OSX, as it turns out, update to Boehm GC package).

Dima Pasechnik

unread,
Dec 6, 2017, 5:09:03 AM12/6/17
to sage-devel
Now I believe that we have a full fix for this: https://trac.sagemath.org/ticket/24015
(so you could install it and use it now, at your own risk :-))
Reply all
Reply to author
Forward
0 new messages