Re: [sage-devel] Re: ecl build failure when building sage

[Dima Pasechnik]

On Fri, Apr 3, 2020 at 11:04 PM Jakub Jabłoński  wrote:
>
> Sorry, didn't notice it's not rebuilding. Done it now and issue with omp 
> still occurs.

hmm. Somewhere something instists on using openmp.

Perhaps, do

make distclean
make

>
> On Friday, April 3, 2020 at 4:13:39 PM UTC+2, Dima Pasechnik wrote:
>>
>> have you rebuilt fflas-ffpack after your addition of flags?
>>
>> On Fri, Apr 3, 2020 at 10:00 PM Jakub Jabłoński  wrote:
>> >
>> > Current version:
>> >
>> > # If SAGE_FAT_BINARY is set, disable all processor-specific optimizations
>> > if [ "$SAGE_FAT_BINARY" = yes ]; then
>> > FFLAS_FFPACK_CONFIGURE="--disable-sse --disable-sse2 --disable-sse3 
>> > --disable-ssse3 --disable-sse41 --disable-sse42 --disable-fma 
>> > --disable-fma4 --disable-avx --disable-avx2 --disable-avx512f 
>> > --disable-avx512dq --disable-avx512vl $FFLAS_FFPACK_CONFIGURE"
>> > fi
>> >
>> > FFLAS_FFPACK_CONFIGURE="--disable-openmp $FFLAS_FFPACK_CONFIGURE"
>> >
>> > Still failing
>> >
>> >
>> > On Friday, April 3, 2020 at 2:00:13 PM UTC+2, Dima Pasechnik wrote:
>> >>
>> >> it seems that your addition is conditional on SAGE_FAT_BINARY being set 
>> >> to yes.
>> >>
>> >> It should not be so.
>> >>
>> >> On Fri, 3 Apr 2020, 19:56 Jakub Jabłoński,  wrote:
>> >>>
>> >>> I have added --disable-openmp here in spkg-install.in:
>> >>> if [ "$SAGE_FAT_BINARY" = yes ]; then
>> >>> FFLAS_FFPACK_CONFIGURE="--disable-openmp --disable-sse 
>> >>> --disable-sse2 --disable-sse3 --disable-ssse3 --disable-sse41 
>> >>> --disable-sse42 --disable-fma --disable-fma4 --disable-avx 
>> >>> --disable-avx2 --disable-avx512f --disable-avx512dq --disable-avx512vl 
>> >>> $FFLAS_FFPACK_CONFIGURE"
>> >>> fi
>> >>>
>> >>> Previous log is after adding that, new log
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> On Friday, April 3, 2020 at 12:46:49 PM UTC+2, Jakub Jabłoński wrote:
>> 
>> 
>> 
>>  On Friday, April 3, 2020 at 11:57:29 AM UTC+2, Dima Pasechnik wrote:
>> >
>> > could you post the top-level config.log ?
>> >
>> >
>> > On Fri, 3 Apr 2020 at 16:59, Dima Pasechnik  wrote:
>> >>
>> >> you are building fflas-ffpack with OpenMP on, for some reason.
>> >> it should be possible to modify its spkg-install.in file so that it 
>> >> does not happen, rebuild it, and sagelib itself.
>> >>
>> >>
>> >> On Fri, 3 Apr 2020 at 16:40, Jakub Jabłoński  wrote:
>> >>>
>> >>> Okay, uploaded only log which seems to be relevant (it's failing)
>> >>>
>> >>> --
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>> >>>
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Re: [sage-devel] Suggestion: Remove restriction on q in NonisotropicOrthogonalPolarGraph

[Ferdinand Ihringer]

I forgot a minor remark.

On Freitag, 3. April 2020 19:13:50 CEST Dima Pasechnik wrote:
> On Sat, Apr 4, 2020 at 12:44 AM Ferdinand Ihringer
>  wrote:
> > My understanding is that I should ask for improvements here. Can one
> > remove the restriction on q in NonisotropicOrthogonalPolarGraph in
> > graphs/generators/classical_geometries.py? These graphs are nice for
> > general q, see [1] or [2].
> IIRC this restriction is due to these graphs not being strongly
> regular for the other values of q.

For m odd and q = 3, you also get SRGs. The SRGs are isomorphic to the 
perp=False case (maybe the complement graph of the perp=False case, do not 
recall).

Best,

Ferdinand



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Re: [sage-devel] Suggestion: Remove restriction on q in NonisotropicOrthogonalPolarGraph

[Ferdinand Ihringer]

Hi Dima,

On Freitag, 3. April 2020 19:13:50 CEST Dima Pasechnik wrote:
> On Sat, Apr 4, 2020 at 12:44 AM Ferdinand Ihringer
>  wrote:
> Certainly we can make that function more general, and test for the
> strongly regular needs elsewhere.

That would be nice.

> (although functions with names starting from _ are not meant for general
> use...)

I only edited classical_geometries.py as it was the quickest solution for me. 
I do not assume that I am meant to edit anything in that file. ;-)

For q odd, just replacing the hard coded point_type by some equivalent of the 
GAP code Difference(List(Elements(GF(q)), x -> x^2), [0 * Z(q)]), respectively, 
Difference(Elements(GF(q)), List(Elements(GF(q)), x -> x^2)) should suffice.

For q even, it is similar with the trace, but I cannot write down GAP code for 
it without some effort.

> If you can open a trac ticket for this, please do and CC me on this

Done. I CCed you in it.

https://trac.sagemath.org/ticket/29459

> (incidentally I am working on https://trac.sagemath.org/ticket/26513
> right now - and appear to have a fix :-))

Nice!

Best,

Ferdinand



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Re: [sage-devel] Re: Sage upgrade issue

[Dima Pasechnik]

On Sat, Apr 4, 2020 at 1:06 AM Ethan Lin  wrote:
>
> So is it the master branch or the develop branch? and git push right?

it's develop branch (master is for releases), and it's pull, not push.

>
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Re: [sage-devel] Suggestion: Remove restriction on q in NonisotropicOrthogonalPolarGraph

[Dima Pasechnik]

Hi Ferdinand,

On Sat, Apr 4, 2020 at 12:44 AM Ferdinand Ihringer
 wrote:
>
> My understanding is that I should ask for improvements here. Can one remove 
> the restriction on q in NonisotropicOrthogonalPolarGraph in 
> graphs/generators/classical_geometries.py? These graphs are nice for general 
> q, see [1] or [2].

IIRC this restriction is due to these graphs not being strongly
regular for the other values of q.
Certainly we can make that function more general, and test for the
strongly regular needs elsewhere.
(although functions with names starting from _ are not meant for general use...)

If you can open a trac ticket for this, please do and CC me on this
(incidentally I am working on https://trac.sagemath.org/ticket/26513
right now - and appear to have a fix :-))



>
> My current hack is to change
>
> if m % 2 == 0:
> if q in [2, 3]:
> G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1])
> else:
> raise ValueError("for m even q must be 2 or 3")
>
> to
>
> if m % 2 == 0:
> if q in [2, 3]:
> G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1])
> elif q == 5:
> G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1,4])
> elif q == 7:
> G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1,2,4])
> else:
> raise ValueError("for m even q must be 2 or 3")
>
> but maybe one can do this more properly in Sage itself? For q odd and m even, 
> point_type should simply be the set of all squares in GF(q). For q odd and m 
> odd (I did not copy this part in the code snippet above), it is either the 
> set of all squares or the set of all non-squares.
>
> For q even, one replaces square/non-square with the trace to distinguish.
>
> I never use Sage's GAP interface (usually, I use GAP directly), but I suspect 
> that anymore slightly more familiar can do this in a minute.
>
> All the best,
>
> Ferdinand
>
>
> [1] https://www.sciencedirect.com/science/article/pii/009731659090029V
> [2] https://arxiv.org/abs/1905.04677 or 
> https://link.springer.com/article/10.1007/s00493-020-4226-6
>
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Re: [sage-devel] Re: Sage upgrade issue

[Ethan Lin]

So is it the master branch or the develop branch? and git push right?

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Re: [sage-devel] Re: Sage upgrade issue

[Dima Pasechnik]

On Sat, Apr 4, 2020 at 12:57 AM Ethan Lin  wrote:
>
> sabe-9.1.beta8 on Ubuntu Linux 20.04 LTS Focal Fossa

Did you install it from source?
If so, then use git to get an update, then run

./bootstrap
make

otherwise, if it was binary, get a newer binary.

>
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[sage-devel] Sage upgrade issue

[Ethan Lin]

sage-9.1.beta8 on Ubuntu Linux 20.04 LTS Focal Fossa.

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[sage-devel] Re: Sage upgrade issue

[Ethan Lin]

sabe-9.1.beta8 on Ubuntu Linux 20.04 LTS Focal Fossa

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Re: [sage-devel] Sage upgrade issue

[Dima Pasechnik]

sage -upgrade is obsolete and should be removed.
It's better to install a new version from source.

On Sat, Apr 4, 2020 at 12:45 AM Ethan Lin  wrote:
>
> Somehow I can seem to upgrade sage with the sage -upgrade command it gives me 
> this error: error: cannot open .git/FETCH_HEAD: Permission denied
>
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[sage-devel] Sage upgrade issue

[Ethan Lin]

Somehow I can seem to upgrade sage with the sage -upgrade command it gives 
me this error: error: cannot open .git/FETCH_HEAD: Permission denied

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[sage-devel] Suggestion: Remove restriction on q in NonisotropicOrthogonalPolarGraph

[Ferdinand Ihringer]

Dear Sage Developers,

My understanding is that I should ask for improvements here. Can one remove 
the restriction on q in NonisotropicOrthogonalPolarGraph in 
graphs/generators/classical_geometries.py? These graphs are nice for 
general q, see [1] or [2].

My current hack is to change

if m % 2 == 0:
if q in [2, 3]:
G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1])
else:
raise ValueError("for m even q must be 2 or 3")

to

if m % 2 == 0:
if q in [2, 3]:
G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1])
elif q == 5:
G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1,4])
elif q == 7:
G = _orthogonal_polar_graph(m, q, sign=sign, point_type=[1,2,4])
else:
raise ValueError("for m even q must be 2 or 3")

but maybe one can do this more properly in Sage itself? For q odd and m 
even, point_type should simply be the set of all squares in GF(q). For q 
odd and m odd (I did not copy this part in the code snippet above), it is 
either the set of all squares or the set of all non-squares.

For q even, one replaces square/non-square with the trace to distinguish.

I never use Sage's GAP interface (usually, I use GAP directly), but I 
suspect that anymore slightly more familiar can do this in a minute.

All the best,

Ferdinand


[1] https://www.sciencedirect.com/science/article/pii/009731659090029V
[2] https://arxiv.org/abs/1905.04677 or 
https://link.springer.com/article/10.1007/s00493-020-4226-6

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Re: [sage-devel] Re: ecl build failure when building sage

[Jakub Jabłoński]

Sorry, didn't notice it's not rebuilding. Done it now and issue with omp 
still occurs. 

On Friday, April 3, 2020 at 4:13:39 PM UTC+2, Dima Pasechnik wrote:
>
> have you rebuilt fflas-ffpack after your addition of flags? 
>
> On Fri, Apr 3, 2020 at 10:00 PM Jakub Jabłoński  > wrote: 
> > 
> > Current version: 
> > 
> > # If SAGE_FAT_BINARY is set, disable all processor-specific 
> optimizations 
> > if [ "$SAGE_FAT_BINARY" = yes ]; then 
> > FFLAS_FFPACK_CONFIGURE="--disable-sse --disable-sse2 --disable-sse3 
> --disable-ssse3 --disable-sse41 --disable-sse42 --disable-fma 
> --disable-fma4 --disable-avx --disable-avx2 --disable-avx512f 
> --disable-avx512dq --disable-avx512vl $FFLAS_FFPACK_CONFIGURE" 
> > fi 
> > 
> > FFLAS_FFPACK_CONFIGURE="--disable-openmp $FFLAS_FFPACK_CONFIGURE" 
> > 
> > Still failing 
> > 
> > 
> > On Friday, April 3, 2020 at 2:00:13 PM UTC+2, Dima Pasechnik wrote: 
> >> 
> >> it seems that your addition is conditional on SAGE_FAT_BINARY being set 
> to yes. 
> >> 
> >> It should not be so. 
> >> 
> >> On Fri, 3 Apr 2020, 19:56 Jakub Jabłoński,  wrote: 
> >>> 
> >>> I have added --disable-openmp here in spkg-install.in: 
> >>> if [ "$SAGE_FAT_BINARY" = yes ]; then 
> >>> FFLAS_FFPACK_CONFIGURE="--disable-openmp --disable-sse 
> --disable-sse2 --disable-sse3 --disable-ssse3 --disable-sse41 
> --disable-sse42 --disable-fma --disable-fma4 --disable-avx --disable-avx2 
> --disable-avx512f --disable-avx512dq --disable-avx512vl 
> $FFLAS_FFPACK_CONFIGURE" 
> >>> fi 
> >>> 
> >>> Previous log is after adding that, new log 
> >>> 
> >>> 
> >>> 
> >>> 
> >>> On Friday, April 3, 2020 at 12:46:49 PM UTC+2, Jakub Jabłoński wrote: 
>  
>  
>  
>  On Friday, April 3, 2020 at 11:57:29 AM UTC+2, Dima Pasechnik wrote: 
> > 
> > could you post the top-level config.log ? 
> > 
> > 
> > On Fri, 3 Apr 2020 at 16:59, Dima Pasechnik  
> wrote: 
> >> 
> >> you are building fflas-ffpack with OpenMP on, for some reason. 
> >> it should be possible to modify its spkg-install.in file so that 
> it does not happen, rebuild it, and sagelib itself. 
> >> 
> >> 
> >> On Fri, 3 Apr 2020 at 16:40, Jakub Jabłoński  
> wrote: 
> >>> 
> >>> Okay, uploaded only log which seems to be relevant (it's failing) 
> >>> 
> >>> -- 
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>  
>
> >>> 
> >>> -- 
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>  
>
> > 
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>  
>
>

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Re: [sage-devel] Re: ecl build failure when building sage

[Dima Pasechnik]

have you rebuilt fflas-ffpack after your addition of flags?

On Fri, Apr 3, 2020 at 10:00 PM Jakub Jabłoński  wrote:
>
> Current version:
>
> # If SAGE_FAT_BINARY is set, disable all processor-specific optimizations
> if [ "$SAGE_FAT_BINARY" = yes ]; then
> FFLAS_FFPACK_CONFIGURE="--disable-sse --disable-sse2 --disable-sse3 
> --disable-ssse3 --disable-sse41 --disable-sse42 --disable-fma --disable-fma4 
> --disable-avx --disable-avx2 --disable-avx512f --disable-avx512dq 
> --disable-avx512vl $FFLAS_FFPACK_CONFIGURE"
> fi
>
> FFLAS_FFPACK_CONFIGURE="--disable-openmp $FFLAS_FFPACK_CONFIGURE"
>
> Still failing
>
>
> On Friday, April 3, 2020 at 2:00:13 PM UTC+2, Dima Pasechnik wrote:
>>
>> it seems that your addition is conditional on SAGE_FAT_BINARY being set to 
>> yes.
>>
>> It should not be so.
>>
>> On Fri, 3 Apr 2020, 19:56 Jakub Jabłoński,  wrote:
>>>
>>> I have added --disable-openmp here in spkg-install.in:
>>> if [ "$SAGE_FAT_BINARY" = yes ]; then
>>> FFLAS_FFPACK_CONFIGURE="--disable-openmp --disable-sse --disable-sse2 
>>> --disable-sse3 --disable-ssse3 --disable-sse41 --disable-sse42 
>>> --disable-fma --disable-fma4 --disable-avx --disable-avx2 --disable-avx512f 
>>> --disable-avx512dq --disable-avx512vl $FFLAS_FFPACK_CONFIGURE"
>>> fi
>>>
>>> Previous log is after adding that, new log
>>>
>>>
>>>
>>>
>>> On Friday, April 3, 2020 at 12:46:49 PM UTC+2, Jakub Jabłoński wrote:



 On Friday, April 3, 2020 at 11:57:29 AM UTC+2, Dima Pasechnik wrote:
>
> could you post the top-level config.log ?
>
>
> On Fri, 3 Apr 2020 at 16:59, Dima Pasechnik  wrote:
>>
>> you are building fflas-ffpack with OpenMP on, for some reason.
>> it should be possible to modify its spkg-install.in file so that it does 
>> not happen, rebuild it, and sagelib itself.
>>
>>
>> On Fri, 3 Apr 2020 at 16:40, Jakub Jabłoński  wrote:
>>>
>>> Okay, uploaded only log which seems to be relevant (it's failing)
>>>
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Re: [sage-devel] Re: ecl build failure when building sage

[Dima Pasechnik]

it seems that your addition is conditional on SAGE_FAT_BINARY being set to
yes.

It should not be so.

On Fri, 3 Apr 2020, 19:56 Jakub Jabłoński,  wrote:

> I have added --disable-openmp here in spkg-install.in:
> if [ "$SAGE_FAT_BINARY" = yes ]; then
> FFLAS_FFPACK_CONFIGURE="--disable-openmp --disable-sse --disable-sse2
> --disable-sse3 --disable-ssse3 --disable-sse41 --disable-sse42
> --disable-fma --disable-fma4 --disable-avx --disable-avx2 --disable-avx512f
> --disable-avx512dq --disable-avx512vl $FFLAS_FFPACK_CONFIGURE"
> fi
>
> Previous log is after adding that, new log
>
>
>
>
> On Friday, April 3, 2020 at 12:46:49 PM UTC+2, Jakub Jabłoński wrote:
>>
>>
>>
>> On Friday, April 3, 2020 at 11:57:29 AM UTC+2, Dima Pasechnik wrote:
>>>
>>> could you post the top-level config.log ?
>>>
>>>
>>> On Fri, 3 Apr 2020 at 16:59, Dima Pasechnik  wrote:
>>>
 you are building fflas-ffpack with OpenMP on, for some reason.
 it should be possible to modify its spkg-install.in file so that it
 does not happen, rebuild it, and sagelib itself.


 On Fri, 3 Apr 2020 at 16:40, Jakub Jabłoński  wrote:

> Okay, uploaded only log which seems to be relevant (it's failing)
>
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> 
> .
>
 --
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> 
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Re: [sage-devel] Re: ecl build failure when building sage

[Jakub Jabłoński]

I have added --disable-openmp here in spkg-install.in:
if [ "$SAGE_FAT_BINARY" = yes ]; then
FFLAS_FFPACK_CONFIGURE="--disable-openmp --disable-sse --disable-sse2 
--disable-sse3 --disable-ssse3 --disable-sse41 --disable-sse42 
--disable-fma --disable-fma4 --disable-avx --disable-avx2 --disable-avx512f 
--disable-avx512dq --disable-avx512vl $FFLAS_FFPACK_CONFIGURE"
fi

Previous log is after adding that, new log




On Friday, April 3, 2020 at 12:46:49 PM UTC+2, Jakub Jabłoński wrote:
>
>
>
> On Friday, April 3, 2020 at 11:57:29 AM UTC+2, Dima Pasechnik wrote:
>>
>> could you post the top-level config.log ?
>>
>>
>> On Fri, 3 Apr 2020 at 16:59, Dima Pasechnik  wrote:
>>
>>> you are building fflas-ffpack with OpenMP on, for some reason.
>>> it should be possible to modify its spkg-install.in file so that it 
>>> does not happen, rebuild it, and sagelib itself.
>>>
>>>
>>> On Fri, 3 Apr 2020 at 16:40, Jakub Jabłoński  wrote:
>>>
 Okay, uploaded only log which seems to be relevant (it's failing)

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 https://groups.google.com/d/msgid/sage-devel/6ae55f28-f271-4486-8d23-4c5f802ef5fc%40googlegroups.com
  
 
 .

>>>

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Re: [sage-devel] Re: ecl build failure when building sage

[Dima Pasechnik]

could you post the top-level config.log ?


On Fri, 3 Apr 2020 at 16:59, Dima Pasechnik  wrote:

> you are building fflas-ffpack with OpenMP on, for some reason.
> it should be possible to modify its spkg-install.in file so that it does
> not happen, rebuild it, and sagelib itself.
>
>
> On Fri, 3 Apr 2020 at 16:40, Jakub Jabłoński  wrote:
>
>> Okay, uploaded only log which seems to be relevant (it's failing)
>>
>> --
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>> "sage-devel" group.
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>> email to sage-devel+unsubscr...@googlegroups.com.
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>> https://groups.google.com/d/msgid/sage-devel/6ae55f28-f271-4486-8d23-4c5f802ef5fc%40googlegroups.com
>> 
>> .
>>
>

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Re: [sage-devel] Re: ecl build failure when building sage

[Dima Pasechnik]

you are building fflas-ffpack with OpenMP on, for some reason.
it should be possible to modify its spkg-install.in file so that it does
not happen, rebuild it, and sagelib itself.


On Fri, 3 Apr 2020 at 16:40, Jakub Jabłoński  wrote:

> Okay, uploaded only log which seems to be relevant (it's failing)
>
> --
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> https://groups.google.com/d/msgid/sage-devel/6ae55f28-f271-4486-8d23-4c5f802ef5fc%40googlegroups.com
> 
> .
>

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Re: [sage-devel] Re: ecl build failure when building sage

[Dima Pasechnik]

from this part of the log it is not possible to see much, except that
Sage's Python library has failed to build.

Please paste as many lines above these from the output as you can.


On Fri, 3 Apr 2020, 15:09 Jakub Jabłoński,  wrote:

> I have removed whole cygwin and reinstalled everything, now ecl is not
> failing. However sage is still not building.
> Building log ends with following text (can't upload logs as attachment,
> don't know why)
> [sagelib-9.1.beta9] collect2: error: ld returned 1 exit status
> [sagelib-9.1.beta9] error: command 'g++' failed with exit status 1
> [sagelib-9.1.beta9] make[4]: *** [Makefile:33: sage] Error 1
> [sagelib-9.1.beta9] make[4]: Leaving directory '/home/Kuba/sage/src'
> [sagelib-9.1.beta9]
> [sagelib-9.1.beta9] real 7m43.455s
> [sagelib-9.1.beta9] user 17m51.494s
> [sagelib-9.1.beta9] sys 0m56.723s
> make[3]: *** [Makefile:1942: sagelib] Error 2
> make[3]: Leaving directory '/home/Kuba/sage/build/make'
> make[2]: *** [Makefile:1801: all-start] Error 2
> make[2]: Leaving directory '/home/Kuba/sage/build/make'
>
> real 7m56.612s
> user 17m56.122s
> sys 1m5.057s
> ***
> Error building Sage.
>
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> 
> .
>

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[sage-devel] Re: ecl build failure when building sage

[Jakub Jabłoński]

I have removed whole cygwin and reinstalled everything, now ecl is not 
failing. However sage is still not building. 
Building log ends with following text (can't upload logs as attachment, 
don't know why)
[sagelib-9.1.beta9] collect2: error: ld returned 1 exit status
[sagelib-9.1.beta9] error: command 'g++' failed with exit status 1
[sagelib-9.1.beta9] make[4]: *** [Makefile:33: sage] Error 1
[sagelib-9.1.beta9] make[4]: Leaving directory '/home/Kuba/sage/src'
[sagelib-9.1.beta9] 
[sagelib-9.1.beta9] real 7m43.455s
[sagelib-9.1.beta9] user 17m51.494s
[sagelib-9.1.beta9] sys 0m56.723s
make[3]: *** [Makefile:1942: sagelib] Error 2
make[3]: Leaving directory '/home/Kuba/sage/build/make'
make[2]: *** [Makefile:1801: all-start] Error 2
make[2]: Leaving directory '/home/Kuba/sage/build/make'

real 7m56.612s
user 17m56.122s
sys 1m5.057s
***
Error building Sage.

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[sage-devel] Re: ecl build failure when building sage

[Jakub Jabłoński]

I have removed whole cygwin and reinstalled everything, now ecl is not 
failing. However sage is still not building. 

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