Re: [sage-devel] Issues installing the optional "libhomfly" package

[Dima Pasechnik]

It's fixed for OSX now, it's the packaging (and the necessary for OSX, as 
it turns out, update to Boehm GC package).
https://github.com/dimpase/libhomfly


On Thursday, October 12, 2017 at 10:29:46 AM UTC+1, Dima Pasechnik wrote:
>
> 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...
>
> On Wednesday, October 11, 2017 at 11:27:07 PM UTC+1, Dima Pasechnik wrote:
>>
>> I can reproduce this linking error on OSX; I've opened #24015 
>>  to track this error.
>>
>>
>> On Wednesday, October 11, 2017 at 10:31:16 AM UTC+1, Erik Bray wrote:
>>>
>>> On Tue, Oct 10, 2017 at 7:51 PM, Jesse H  wrote: 
>>> > 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. 
>>>
>>> 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 
>>>
>>

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Re: [sage-devel] Issues installing the optional "libhomfly" package

[Dima Pasechnik]

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...

On Wednesday, October 11, 2017 at 11:27:07 PM UTC+1, Dima Pasechnik wrote:
>
> I can reproduce this linking error on OSX; I've opened #24015 
>  to track this error.
>
>
> On Wednesday, October 11, 2017 at 10:31:16 AM UTC+1, Erik Bray wrote:
>>
>> On Tue, Oct 10, 2017 at 7:51 PM, Jesse H  wrote: 
>> > 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. 
>>
>> 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 
>>
>

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Re: [sage-devel] Issues installing the optional "libhomfly" package

[Dima Pasechnik]

I can reproduce this linking error on OSX; I've opened #24015 
 to track this error.


On Wednesday, October 11, 2017 at 10:31:16 AM UTC+1, Erik Bray wrote:
>
> On Tue, Oct 10, 2017 at 7:51 PM, Jesse H > 
> wrote: 
> > 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. 
>
> 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 
>

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Re: [sage-devel] Issues installing the optional "libhomfly" package

[Erik Bray]

On Tue, Oct 10, 2017 at 7:51 PM, Jesse H  wrote:
> 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.

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

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Re: [sage-devel] Issues installing the optional "libhomfly" package

[Erik Bray]

On Tue, Oct 10, 2017 at 8:31 PM, Dima Pasechnik  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.

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[sage-devel] Issues installing the optional "libhomfly" package

[Dima Pasechnik]

although the linking error you got seems to be not related to GC.

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[sage-devel] Issues installing the optional "libhomfly" package

[Dima Pasechnik]

to install Boehm GC Sage package, do

sage -i gc

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[sage-devel] Issues installing the optional "libhomfly" package

[Jesse H]

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

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Found local metadata for libhomfly-1.0r2
Attempting to download package libhomfly-1.0r2.tar.gz from mirrors
http://files.sagemath.org/spkg/upstream/libhomfly/libhomfly-1.0r2.tar.gz
[..]
libhomfly-1.0r2

Setting up build directory for libhomfly-1.0r2
Finished extraction
No patch files found in ../patches

Host system:
Darwin Jesses-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 
17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64

C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Applications/SageMath-8.0.app/Contents/Resources/sage/local/libexec/gcc/x86_64-apple-darwin15.6.0/5.4.0/lto-wrapper
Target: x86_64-apple-darwin15.6.0
Configured with: ../src/configure 
--prefix=/Applications/SageMath-8.0.app/Contents/Resources/sage/local 
--with-local-prefix=/Applications/SageMath-8.0.app/Contents/Resources/sage/local
 --with-gmp=/Applications/SageMath-8.0.app/Contents/Resources/sage/local 
--with-mpfr=/Applications/SageMath-8.0.app/Contents/Resources/sage/local 
--with-mpc=/Applications/SageMath-8.0.app/Contents/Resources/sage/local 
--with-system-zlib --disable-multilib --disable-nls 
--enable-languages=c,c++,fortran --disable-libitm 
--with-build-config=bootstrap-debug --without-isl --without-cloog  
Thread model: posix
gcc version 5.4.0 (GCC) 

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... build-aux/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking the archiver (ar) interface... ar
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking build system type... x86_64-apple-darwin16.7.0
checking host system type... x86_64-apple-darwin16.7.0
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... ld
checking if the linker (ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin16.7.0 file names to 
x86_64-apple-darwin16.7.0 format... func_convert_file_