compile problem for sage 9.2.b9 on mac 11.0 big sur

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David Joyner

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Aug 22, 2020, 3:06:24 PM8/22/20
to SAGE support, David Joyner
Hi:

I don't know if this has been discussed yet but
I just upgraded to mac os 11.0. I downloaded
sage 9.2.b9 and ran make. I got a "you must
run ./configure first message, which I did.
Then I ran make and the compilation stopped while
compiling python 3. The log is attached.

- David Joyner


install.log

Dima Pasechnik

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Aug 22, 2020, 3:28:22 PM8/22/20
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note: 'utimensat' has been marked as being introduced in macOS 10.13
here, but the deployment target is macOS 10.9.0

seems to indicate that one has to properly set MACOS_DEPLOYMENT_TARGET
(or a suchlike thing) to 10.13 or even bigger.
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Dima Pasechnik

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Aug 22, 2020, 4:52:34 PM8/22/20
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On Sat, Aug 22, 2020 at 8:28 PM Dima Pasechnik <dim...@gmail.com> wrote:
>
> note: 'utimensat' has been marked as being introduced in macOS 10.13
> here, but the deployment target is macOS 10.9.0
>
> seems to indicate that one has to properly set MACOS_DEPLOYMENT_TARGET
> (or a suchlike thing) to 10.13 or even bigger.

indeed, in src/bin/sage-env on has

MACOSX_DEPLOYMENT_TARGET=10.9

which is the reason for that error, I guess.

David Joyner

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Aug 22, 2020, 5:51:08 PM8/22/20
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On Sat, Aug 22, 2020 at 4:52 PM Dima Pasechnik <dim...@gmail.com> wrote:
On Sat, Aug 22, 2020 at 8:28 PM Dima Pasechnik <dim...@gmail.com> wrote:
>
> note: 'utimensat' has been marked as being introduced in macOS 10.13
> here, but the deployment target is macOS 10.9.0
>
> seems to indicate that one has to properly set MACOS_DEPLOYMENT_TARGET
> (or a suchlike thing) to 10.13 or even bigger.

indeed, in src/bin/sage-env on has

MACOSX_DEPLOYMENT_TARGET=10.9

which is the reason for that error, I guess.

Shouldn't it be 11.0?

I changed it then tried to recompile but it stopped at the same place.
I can't install a system python3 using homebrew since it's broken

 

>
> On Sat, Aug 22, 2020 at 8:06 PM David Joyner <wdjo...@gmail.com> wrote:
> >
> > Hi:
> >
> > I don't know if this has been discussed yet but
> > I just upgraded to mac os 11.0. I downloaded
> > sage 9.2.b9 and ran make. I got a "you must
> > run ./configure first message, which I did.
> > Then I ran make and the compilation stopped while
> > compiling python 3. The log is attached.
> >
> > - David Joyner
> >
> >
> > --
> > You received this message because you are subscribed to the Google Groups "sage-support" group.
> > To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.
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Dima Pasechnik

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Aug 22, 2020, 6:02:04 PM8/22/20
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On Sat, Aug 22, 2020 at 10:51 PM David Joyner <wdjo...@gmail.com> wrote:
>
>
>
> On Sat, Aug 22, 2020 at 4:52 PM Dima Pasechnik <dim...@gmail.com> wrote:
>>
>> On Sat, Aug 22, 2020 at 8:28 PM Dima Pasechnik <dim...@gmail.com> wrote:
>> >
>> > note: 'utimensat' has been marked as being introduced in macOS 10.13
>> > here, but the deployment target is macOS 10.9.0
>> >
>> > seems to indicate that one has to properly set MACOS_DEPLOYMENT_TARGET
>> > (or a suchlike thing) to 10.13 or even bigger.
>>
>> indeed, in src/bin/sage-env on has
>>
>> MACOSX_DEPLOYMENT_TARGET=10.9
>>
>> which is the reason for that error, I guess.
>
>
> Shouldn't it be 11.0?
>
> I changed it then tried to recompile but it stopped at the same place.
> I can't install a system python3 using homebrew since it's broken
> https://github.com/Homebrew/brew/issues/7803

you can install a binary python3.7 from python.org - this is known to
be possible to use in Sage on macOS 10.15 and earlier versions.

>
>
>>
>>
>> >
>> > On Sat, Aug 22, 2020 at 8:06 PM David Joyner <wdjo...@gmail.com> wrote:
>> > >
>> > > Hi:
>> > >
>> > > I don't know if this has been discussed yet but
>> > > I just upgraded to mac os 11.0. I downloaded
>> > > sage 9.2.b9 and ran make. I got a "you must
>> > > run ./configure first message, which I did.
>> > > Then I ran make and the compilation stopped while
>> > > compiling python 3. The log is attached.
>> > >
>> > > - David Joyner
>> > >
>> > >
>> > > --
>> > > You received this message because you are subscribed to the Google Groups "sage-support" group.
>> > > To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.
>> > > To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAEQuuAVjRasvOnj7NKQGfXxjL2g9XPfi8WFXdO-6A3mZ_XedHg%40mail.gmail.com.
>>
>> --
>> You received this message because you are subscribed to the Google Groups "sage-support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.
>> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq2AU24nTFsL2eq3%3DPYgj5320t2LyQJV%2BRFon%2BhrzLJseA%40mail.gmail.com.
>
> --
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David Joyner

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Aug 22, 2020, 6:23:13 PM8/22/20
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On Sat, Aug 22, 2020 at 6:02 PM Dima Pasechnik <dim...@gmail.com> wrote:
On Sat, Aug 22, 2020 at 10:51 PM David Joyner <wdjo...@gmail.com> wrote:
>
>
>
> On Sat, Aug 22, 2020 at 4:52 PM Dima Pasechnik <dim...@gmail.com> wrote:
>>
>> On Sat, Aug 22, 2020 at 8:28 PM Dima Pasechnik <dim...@gmail.com> wrote:
>> >
>> > note: 'utimensat' has been marked as being introduced in macOS 10.13
>> > here, but the deployment target is macOS 10.9.0
>> >
>> > seems to indicate that one has to properly set MACOS_DEPLOYMENT_TARGET
>> > (or a suchlike thing) to 10.13 or even bigger.
>>
>> indeed, in src/bin/sage-env on has
>>
>> MACOSX_DEPLOYMENT_TARGET=10.9
>>
>> which is the reason for that error, I guess.
>
>
> Shouldn't it be 11.0?
>
> I changed it then tried to recompile but it stopped at the same place.
> I can't install a system python3 using homebrew since it's broken
> https://github.com/Homebrew/brew/issues/7803

you can install a binary python3.7 from python.org - this is known to
be possible to use in Sage on macOS 10.15 and earlier versions.


I installed both python 3.8.5 (the latest) and when that failed 3.7.9.

The end of the output of configure is this seeming contradictory info:

configure: notice: the following SPKGs did not find equivalent system packages: brial cbc cddlib cliquer coxeter3 eclib ecm fflas_ffpack flintqs fplll gf2x gfan givaro glpk gp2c gsl iconv iml lcalc libatomic_ops libbraiding libsemigroups lrcalc m4ri m4rie nauty ninja_build openblas palp pandoc pari pari_elldata pari_galdata pari_galpol pari_nftables pari_seadata pari_seadata_small pcre perl_cpan_polymake_prereq perl_term_readline_gnu planarity ppl python3 r rw suitesparse symmetrica sympow tachyon yasm zeromq zn_poly

checking for the package system in use... unknown

wdj@jeeves sage-9.2.beta9 % which python3   

/usr/local/bin/python3

wdj@jeeves sage-9.2.beta9 % python3 --version

Python 3.7.9

There isn't a python3 system package but there is?
 
>
>
>>
>>
>> >
>> > On Sat, Aug 22, 2020 at 8:06 PM David Joyner <wdjo...@gmail.com> wrote:
>> > >
>> > > Hi:
>> > >
>> > > I don't know if this has been discussed yet but
>> > > I just upgraded to mac os 11.0. I downloaded
>> > > sage 9.2.b9 and ran make. I got a "you must
>> > > run ./configure first message, which I did.
>> > > Then I ran make and the compilation stopped while
>> > > compiling python 3. The log is attached.
>> > >
>> > > - David Joyner
>> > >
>> > >
>> > > --
>> > > You received this message because you are subscribed to the Google Groups "sage-support" group.
>> > > To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.
>> > > To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAEQuuAVjRasvOnj7NKQGfXxjL2g9XPfi8WFXdO-6A3mZ_XedHg%40mail.gmail.com.
>>
>> --
>> You received this message because you are subscribed to the Google Groups "sage-support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.
>> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAAWYfq2AU24nTFsL2eq3%3DPYgj5320t2LyQJV%2BRFon%2BhrzLJseA%40mail.gmail.com.
>
> --
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Dima Pasechnik

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Aug 22, 2020, 6:44:01 PM8/22/20
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On Sat, Aug 22, 2020 at 11:23 PM David Joyner <wdjo...@gmail.com> wrote:
>
>
>
> On Sat, Aug 22, 2020 at 6:02 PM Dima Pasechnik <dim...@gmail.com> wrote:
>>
>> On Sat, Aug 22, 2020 at 10:51 PM David Joyner <wdjo...@gmail.com> wrote:
>> >
>> >
>> >
>> > On Sat, Aug 22, 2020 at 4:52 PM Dima Pasechnik <dim...@gmail.com> wrote:
>> >>
>> >> On Sat, Aug 22, 2020 at 8:28 PM Dima Pasechnik <dim...@gmail.com> wrote:
>> >> >
>> >> > note: 'utimensat' has been marked as being introduced in macOS 10.13
>> >> > here, but the deployment target is macOS 10.9.0
>> >> >
>> >> > seems to indicate that one has to properly set MACOS_DEPLOYMENT_TARGET
>> >> > (or a suchlike thing) to 10.13 or even bigger.
>> >>
>> >> indeed, in src/bin/sage-env on has
>> >>
>> >> MACOSX_DEPLOYMENT_TARGET=10.9
>> >>
>> >> which is the reason for that error, I guess.
>> >
>> >
>> > Shouldn't it be 11.0?
>> >
>> > I changed it then tried to recompile but it stopped at the same place.
>> > I can't install a system python3 using homebrew since it's broken
>> > https://github.com/Homebrew/brew/issues/7803
>>
>> you can install a binary python3.7 from python.org - this is known to
>> be possible to use in Sage on macOS 10.15 and earlier versions.
>>
>
> I installed both python 3.8.5 (the latest) and when that failed 3.7.9.
>
> The end of the output of configure is this seeming contradictory info:
>
> configure: notice: the following SPKGs did not find equivalent system packages: brial cbc cddlib cliquer coxeter3 eclib ecm fflas_ffpack flintqs fplll gf2x gfan givaro glpk gp2c gsl iconv iml lcalc libatomic_ops libbraiding libsemigroups lrcalc m4ri m4rie nauty ninja_build openblas palp pandoc pari pari_elldata pari_galdata pari_galpol pari_nftables pari_seadata pari_seadata_small pcre perl_cpan_polymake_prereq perl_term_readline_gnu planarity ppl python3 r rw suitesparse symmetrica sympow tachyon yasm zeromq zn_poly

This notice is more about ./configure being confused whether there is
Homebrew or Conda installed.

The interesting line of ./configure output is above that notice:

python3-3.7.3.p1: using system package;
SPKG will not be installed

- if it's there then system Python will be used.
Otherwise, look in config.log for more details.

HTH
Dima
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAEQuuAWxr0GJKaNmDjpLHe8wcp7Fgng787gHztyMmV6PKNSEYA%40mail.gmail.com.

John H Palmieri

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Sep 1, 2020, 11:38:47 PM9/1/20
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I've been trying to build on Big Sur, too. I removed the MACOSX_DEPLOYMENT_TARGET lines from sage-env, but the Python build still fails. The log file is attached. Any suggestions (besides installing a different system version of Python)?

  John
python3-3.7.3.p1.log

John H Palmieri

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Sep 1, 2020, 11:59:14 PM9/1/20
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If I do install Python 3.7, then gf2x and ecm both fail to build. The gf2x log file says "configure: error: Cannot find a build system compiler
". The ecm log file says "checking if globals are prefixed by underscore... configure: error: Test program links neither with nor without underscore."

Matthias Koeppe

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Sep 2, 2020, 12:43:15 AM9/2/20
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The issue with "posixmodule" is apparently https://bugs.python.org/issue41100

Matthias Koeppe

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Sep 2, 2020, 12:49:57 AM9/2/20
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This fix was already merged in 3.8.4, so after https://trac.sagemath.org/ticket/27754 we should be fine.

The PR for Python 3.7 is https://github.com/python/cpython/pull/21155, but our Python 3.7.x is very old already.

Matthias Koeppe

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Sep 2, 2020, 12:52:37 AM9/2/20
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On Tuesday, September 1, 2020 at 8:59:14 PM UTC-7, John H Palmieri wrote:
If I do install Python 3.7, then gf2x and ecm both fail to build. The gf2x log file says "configure: error: Cannot find a build system compiler
". The ecm log file says "checking if globals are prefixed by underscore... configure: error: Test program links neither with nor without underscore."


gf2x was just upgraded in https://trac.sagemath.org/ticket/30412 - merged in 9.2.beta11. Did you test with this beta or an earlier one?

 

John H Palmieri

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Sep 2, 2020, 12:59:59 AM9/2/20
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I tried with 9.2.beta10, and just now I tried with this new version of gf2x. Same error either way. Here is the gf2x config.log.

 
config.log

Matthias Koeppe

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Sep 2, 2020, 1:29:52 AM9/2/20
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These lines:
configure:17396: checking build system compiler gcc
etc.
might indicate that the configure script is confused about cross compiling to a different architecture.

John H Palmieri

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Sep 2, 2020, 11:19:37 AM9/2/20
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With a system Python and "make -k", the following packages fail:

gf2x
ecm
symmetrica
rubiks
ecl
scipy

Matthias Koeppe

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Sep 2, 2020, 12:10:21 PM9/2/20
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I also see build failures of at least some of these packages at https://github.com/mkoeppe/sage/runs/1059961873 (using a new GH workflow that runs Xcode 12 beta, added in https://trac.sagemath.org/ticket/30487)

I have opened https://trac.sagemath.org/ticket/30494 "Meta-ticket: Support Xcode 12, macOS 11 Big Sur"

David Joyner

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Sep 17, 2020, 6:12:18 AM9/17/20
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 I downloaded sage 9.2.b12 then ran configure and make using newly upgraded Xcode 12.
Instead of failing at python it fails at readline. The log is attached.

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install.log

Dima Pasechnik

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Sep 17, 2020, 6:54:16 AM9/17/20
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in the log you attached the failure is in python3, and it's dated Aug 22
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAEQuuAV6ybPcOgR36tttkMQ%3DVk2KQRAy1kYXjF234OgkCDUwPQ%40mail.gmail.com.

David Joyner

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Sep 17, 2020, 8:10:02 AM9/17/20
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On Thu, Sep 17, 2020 at 6:54 AM Dima Pasechnik <dim...@gmail.com> wrote:
in the log you attached the failure is in python3, and it's dated Aug 22


Wrong log! Sorry!
The correct one is attached I hope:-)
 
install.log

Dima Pasechnik

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Sep 17, 2020, 8:24:27 AM9/17/20
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try upgrading to the latest readline (8.0.4), e.g. install as much as
possible from Homebrew,
which has this version working.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CAEQuuAUcBC2P1yNL-chah6%3Ds-izrXHoeQMDmPYHb_xKWZV%3DSKg%40mail.gmail.com.

David Joyner

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Sep 17, 2020, 10:15:06 AM9/17/20
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On Thu, Sep 17, 2020 at 8:24 AM Dima Pasechnik <dim...@gmail.com> wrote:
try upgrading to the latest readline (8.0.4), e.g. install as much as
possible from Homebrew,
which has this version working.


Done

wdj@jeeves sage-9.2.beta12 % brew upgrade readline
Warning: You are using macOS 11.0.
We do not provide support for this pre-release version.
You will encounter build failures with some formulae.
Please create pull requests instead of asking for help on Homebrew's GitHub,
Discourse, Twitter or IRC. You are responsible for resolving any issues you
experience while you are running this pre-release version.
Warning: readline 8.0.4 already installed
wdj@jeeves sage-9.2.beta12 % which readline      
readline not found
 
Same compiling error:

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):
* package:         readline-6.3.008.p0
  last build time: Sep 17 10:10
  log file:        /Users/wdj/sagefiles/sage-9.2.beta12/logs/pkgs/readline-6.3.008.p0.log
  build directory: /Users/wdj/sagefiles/sage-9.2.beta12/local/var/tmp/sage/build/readline-6.3.008.p0


Maybe make+configure can't find readline?


Dima Pasechnik

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Sep 17, 2020, 10:20:53 AM9/17/20
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the top level config.log will tell you why ./configure did not accept pre-installed readline.

probably you forgot to

source .homebrew...

before 

./configure



 (afk, so don't recall the exact file name, but it is the only one that starts with '.' and has homebrew in)
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