Re: [sage-devel] Re: Help and Advice | Arithmetic of Jacobians in the Split/Real Model is Broken

[Zachary Scherr]

Just wanted to mention that I posted about something similar a few years
ago here:
https://groups.google.com/g/sage-support/c/j1Y9yuu-VuE/m/cA7N8iqCCAAJ.  At
the time a trac ticket was opened, but I'm not sure about the status
especially post the github migration.

On Wed, Mar 6, 2024 at 11:55 AM Nils Bruin  wrote:

> On Wednesday 6 March 2024 at 04:52:16 UTC-8 Giacomo Pope wrote:
>
>
> I think aside from maybe needing additional methods on the hyperelliptic
> curve, once the projective model is right and points on the curve are well
> defined for all cases. I do not have any intuition on whether the balanced
> model will for example have issues with the p-Adic implementation as I have
> no experience in this area.
>
> Tiny bit of feedback on the p-adic bit: as far as I know, things like
> Cantor's algorithm use euclidean division, wwhich is a big problem
> p-adically: coefficients may vanish unexpectedly and p-adically you cannot
> distinguish that from loss of precision. I think that's already a problem
> in the existing implementation and I think it will be in yours as well. So
> I think you can ignore p-adics to begin with. If you can get it working
> usefully and reliably for p-adic base fields as well then that's a real
> win!
>
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> 
> .
>

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[sage-devel] Re: Building Sage 9.3 on Mac fails due to numpy

[Zachary Scherr]

Just as a followup, I did confirm on my Big Sur that the steps I outlined 
above does let sage build.

On Monday, May 10, 2021 at 3:52:20 PM UTC-4 Matthias Koeppe wrote:

> Yes, using gcc@10 from homebrew should be a good option too. I have added 
> this suggestion to  to 
> https://wiki.sagemath.org/ReleaseTours/sage-9.3#Availability_of_Sage_9.3_and_installation_help
>  
> (it may need expanding)
>
> On Monday, May 10, 2021 at 12:28:50 PM UTC-7 zsc...@gmail.com wrote:
>
>> sorry, that should be `brew install gcc@10`
>>
>> On Monday, May 10, 2021 at 3:27:47 PM UTC-4 Zachary Scherr wrote:
>>
>>> I haven't fully tested this yet, but you can also try installing gcc-10 
>>> through homebrew and then using gfortran-10.  Here are the steps to try:
>>>
>>> > brew install gcc-10
>>>
>>> and then once in a clean sage directory (so run make distclean if you 
>>> need to):
>>>
>>> > source .homebrew-build-env
>>> > make configure
>>> > FC=gfortran-10 ./configure
>>> > make
>>>
>>> will force the configure script to use gfortran 10.  At the time of 
>>> posting this I did check that this does allow numpy to build.
>>>
>>>
>>>
>>> On Monday, May 10, 2021 at 3:01:56 PM UTC-4 Matthias Koeppe wrote:
>>>
>>>> Our configure script rejects the current gfortran from homebrew - which 
>>>> is already 11.1.
>>>>
>>>> This leads to building gfortran from source, an old version which does 
>>>> not support Big Sur. 
>>>> Try with https://trac.sagemath.org/ticket/29703 please (use 
>>>> ./bootstrap), which upgrades our gcc/gfortran package.
>>>>
>>>>
>>>>
>>>> On Monday, May 10, 2021 at 11:46:50 AM UTC-7 modp...@gmail.com wrote:
>>>>
>>>>> I'm trying to build SageMath 9.3 from source on MacOS Big Sur 11.3.1.
>>>>>
>>>>> It fails with the following:
>>>>>
>>>>> v = self.gnu_version_match(version_string)
>>>>>
>>>>>   File 
>>>>> "/Users/myUser/app/sage-9.3/local/var/tmp/sage/build/numpy-1.19.5/src/numpy/distutils/fcompiler/gnu.py",
>>>>>  
>>>>> line 80, in gnu_version_match
>>>>>
>>>>> raise ValueError(err + version_string)
>>>>>
>>>>> ValueError: A valid Fortran version was not found in this string:
>>>>>
>>>>>
>>>>> 9.2.0
>>>>>
>>>>>
>>>>> 
>>>>>
>>>>> Error building a wheel for numpy-1.19.5
>>>>>
>>>>>
>>>>> 
>>>>>
>>>>>
>>>>> Please find the log files attached. Any ideas what the issue might be?
>>>>>
>>>>

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[sage-devel] Re: Building Sage 9.3 on Mac fails due to numpy

[Zachary Scherr]

sorry, that should be `brew install gcc@10`

On Monday, May 10, 2021 at 3:27:47 PM UTC-4 Zachary Scherr wrote:

> I haven't fully tested this yet, but you can also try installing gcc-10 
> through homebrew and then using gfortran-10.  Here are the steps to try:
>
> > brew install gcc-10
>
> and then once in a clean sage directory (so run make distclean if you need 
> to):
>
> > source .homebrew-build-env
> > make configure
> > FC=gfortran-10 ./configure
> > make
>
> will force the configure script to use gfortran 10.  At the time of 
> posting this I did check that this does allow numpy to build.
>
>
>
> On Monday, May 10, 2021 at 3:01:56 PM UTC-4 Matthias Koeppe wrote:
>
>> Our configure script rejects the current gfortran from homebrew - which 
>> is already 11.1.
>>
>> This leads to building gfortran from source, an old version which does 
>> not support Big Sur. 
>> Try with https://trac.sagemath.org/ticket/29703 please (use 
>> ./bootstrap), which upgrades our gcc/gfortran package.
>>
>>
>>
>> On Monday, May 10, 2021 at 11:46:50 AM UTC-7 modp...@gmail.com wrote:
>>
>>> I'm trying to build SageMath 9.3 from source on MacOS Big Sur 11.3.1.
>>>
>>> It fails with the following:
>>>
>>> v = self.gnu_version_match(version_string)
>>>
>>>   File 
>>> "/Users/myUser/app/sage-9.3/local/var/tmp/sage/build/numpy-1.19.5/src/numpy/distutils/fcompiler/gnu.py",
>>>  
>>> line 80, in gnu_version_match
>>>
>>> raise ValueError(err + version_string)
>>>
>>> ValueError: A valid Fortran version was not found in this string:
>>>
>>>
>>> 9.2.0
>>>
>>>
>>> 
>>>
>>> Error building a wheel for numpy-1.19.5
>>>
>>>
>>> 
>>>
>>>
>>> Please find the log files attached. Any ideas what the issue might be?
>>>
>>

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[sage-devel] Re: Building Sage 9.3 on Mac fails due to numpy

[Zachary Scherr]

I haven't fully tested this yet, but you can also try installing gcc-10 
through homebrew and then using gfortran-10.  Here are the steps to try:

> brew install gcc-10

and then once in a clean sage directory (so run make distclean if you need 
to):

> source .homebrew-build-env
> make configure
> FC=gfortran-10 ./configure
> make

will force the configure script to use gfortran 10.  At the time of posting 
this I did check that this does allow numpy to build.



On Monday, May 10, 2021 at 3:01:56 PM UTC-4 Matthias Koeppe wrote:

> Our configure script rejects the current gfortran from homebrew - which is 
> already 11.1.
>
> This leads to building gfortran from source, an old version which does not 
> support Big Sur. 
> Try with https://trac.sagemath.org/ticket/29703 please (use ./bootstrap), 
> which upgrades our gcc/gfortran package.
>
>
>
> On Monday, May 10, 2021 at 11:46:50 AM UTC-7 modp...@gmail.com wrote:
>
>> I'm trying to build SageMath 9.3 from source on MacOS Big Sur 11.3.1.
>>
>> It fails with the following:
>>
>> v = self.gnu_version_match(version_string)
>>
>>   File 
>> "/Users/myUser/app/sage-9.3/local/var/tmp/sage/build/numpy-1.19.5/src/numpy/distutils/fcompiler/gnu.py",
>>  
>> line 80, in gnu_version_match
>>
>> raise ValueError(err + version_string)
>>
>> ValueError: A valid Fortran version was not found in this string:
>>
>>
>> 9.2.0
>>
>>
>> 
>>
>> Error building a wheel for numpy-1.19.5
>>
>>
>> 
>>
>>
>> Please find the log files attached. Any ideas what the issue might be?
>>
>

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Re: [sage-devel] Trouble building cython

[Zachary Scherr]

I see that the link I posted to the installation from source documentation 
doesn't mention autoconf/automake, but I would have thought some other 
package would have already installed them.  Probably since homebrew is all 
bottles now they don't automatically get installed anymore if you are not 
building locally.

But Dima is right, it's probably best practice to brew install the packages 
listed in the file build/pkgs/_bootstrap/distros/homebrew.txt.



On Tuesday, February 9, 2021 at 10:43:00 AM UTC-5 dim...@gmail.com wrote:

> On Tue, Feb 9, 2021 at 3:32 PM Trevor Karn  wrote:
> >
> > I uninstalled and reinstalled homebrew and that got rid of the brew 
> doctor warnings. I then brewed the suggested packages from the Sage link 
> Zachary provided and the packages listed at the end of the output of 
> configure.
> >
> > Then from SAGE_ROOT I ran
> >
> > make distclean
> > source .homebrew-build-env
> > ./bootstrap -d
> > ./configure
> > make -j4 build
> >
> > In the end this seems to be working. Thank you so much Dima and Zachary 
> for your help.
> >
> > The reason for running ./bootstrap with the -d flag was because that is 
> what an error message told me to do. Without -d flag:
> >
> > trevorkarn@Trevors-MacBook-Air sage % source .homebrew-build-env
> >
> > trevorkarn@Trevors-MacBook-Air sage % ./bootstrap
> >
> > rm -rf config configure build/make/Makefile-auto.in
> >
> > rm -f src/doc/en/installation/*.txt
> >
> > rm -rf src/doc/en/reference/spkg/*.rst
> >
> > rm -f src/doc/en/reference/repl/*.txt
> >
> > rm -f environment.yml
> >
> > rm -f src/environment.yml
> >
> > rm -f environment-optional.yml
> >
> > rm -f src/environment-optional.yml
> >
> > src/doc/bootstrap:92: installing src/doc/en/installation/arch.txt and 
> src/doc/en/installation/arch-optional.txt
> >
> > src/doc/bootstrap:92: installing src/doc/en/installation/debian.txt and 
> src/doc/en/installation/debian-optional.txt
> >
> > src/doc/bootstrap:92: installing src/doc/en/installation/fedora.txt and 
> src/doc/en/installation/fedora-optional.txt
> >
> > src/doc/bootstrap:92: installing src/doc/en/installation/cygwin.txt and 
> src/doc/en/installation/cygwin-optional.txt
> >
> > src/doc/bootstrap:92: installing src/doc/en/installation/homebrew.txt 
> and src/doc/en/installation/homebrew-optional.txt
> >
> > src/doc/bootstrap:66: installing environment.yml, 
> environment-optional.yml, src/environment.yml and 
> src/environment-optional.yml
> >
> > src/doc/bootstrap:103: installing src/doc/en/reference/spkg/*.rst
> >
> > src/doc/bootstrap:182: installing src/doc/en/reference/repl/options.txt
> >
> > bootstrap:73: installing 'config/config.rpath'
> >
> > ./bootstrap: line 118: aclocal: command not found
> >
> > Bootstrap failed. Either install autotools or run bootstrap with
> >
> > the -d option to download the auto-generated files instead.
>
> build/pkgs/_bootstrap/distros/homebrew.txt
>
> contains a list of dev packages recommended for Homebrew.
> (and with these installed, ./bootstrap should complete without errors)
>
> I wonder whether any of these are printed at the end of the ./configure 
> run.
>
>
> >
> >
> > Best Regards,
> >
> > Trevor Karn
> >
> >
> > On Tue, Feb 9, 2021 at 4:06 AM Dima Pasechnik  wrote:
> >>
> >> On Tue, Feb 9, 2021 at 4:07 AM Zachary Scherr  wrote:
> >> >
> >> > I need to sign off for the night, but the numpy error is definitely 
> related to gfortran. If you have gcc installed via homebrew then it should 
> come with the latest version of gfortran. You can see from your config.log 
> file that gfortran is not found:
> >> >
> >> > configure:7281: checking for gfortran
> >> > configure:7311: result: no
> >> >
> >> > and other standard homebrew packages are not found, like openblas:
> >> >
> >> > configure:12171: checking BLAS library
> >> > configure:12190: result: openblas
> >> > configure:12239: checking whether any of gfortran is installed as or 
> will be installed as SPKG
> >> > configure:12243: result: yes; install openblas as well
> >> > configure:13540: no suitable system package found for SPKG openblas
> >> >
> >> > are you aware if you have gcc and openblas installed via homebrew? I 
> also see that you didn't run "source .homebrew-build-env" before running 
> ./configure since I don't see certain items on your pat

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

I need to sign off for the night, but the numpy error is definitely related 
to gfortran.  If you have gcc installed via homebrew then it should come 
with the latest version of gfortran.  You can see from your config.log file 
that gfortran is not found:

configure:7281: checking for gfortran
configure:7311: result: no

and other standard homebrew packages are not found, like openblas:

configure:12171: checking BLAS library
configure:12190: result: openblas
configure:12239: checking whether any of gfortran is installed as or will 
be installed as SPKG
configure:12243: result: yes; install openblas as well
configure:13540: no suitable system package found for SPKG openblas

are you aware if you have gcc and openblas installed via homebrew? I also 
see that you didn't run "source .homebrew-build-env" before running 
./configure since I don't see certain items on your path.  If you go to the 
sage installation guide 
at 
https://doc.sagemath.org/html/en/installation/source.html#macos-recommended-installation
 
you can see a list of homebrew packages you might want to have before 
installing sage.  I think if you get everything in working order with 
homebrew then you shouldn't have any issues installing sage.  Here is my 
best suggestion as to what to try:

- fix all "brew doctor" warnings.  This might not be necessary, but I get 
worried when I see so many warnings.  You can probably just delete all the 
suggested files and you should be fine.

- install all the recommended homebrew packages.  If any are already 
installed then maybe try "brew reinstall" to make sure it is installed 
properly.  If you think you have homebrew gcc installed then you should be 
able to do "which gfortran" and "gfortran --version".  That should 
hopefully show you that you have gfortran 10.2.0_3.

- in your sage folder under the develop branch you should run the commands 
I mentioned, and don't skip out on "source .homebrew-build-env":

>> make distclean
>> ./bootstrap
>> source .homebrew-build-env
>> ./configure

Before running "make -j4 build" you can look at config.log and make sure 
that it picked up all of the relevant homebrew packages.





On Monday, February 8, 2021 at 10:52:43 PM UTC-5 Trevor Karn wrote:

> Here is the new one. Thanks so much for all of your help on this, Zachary.
>
>
> Best Regards,
>
> Trevor Karn
>
>
> On Mon, Feb 8, 2021 at 9:40 PM Zachary Scherr  wrote:
>
>> At some point you should deal with those warnings, but I don't think that 
>> is what is causing your problems (although they are probably symptomatic of 
>> other possible issues).  
>>
>> The config.log file you posted earlier is picking up a lot of packages 
>> that were built by sage and not from homebrew.  Do you have the config.log 
>> file that you got after running make distclean? 
>>
>> On Monday, February 8, 2021 at 10:10:01 PM UTC-5 Trevor Karn wrote:
>>
>>> brew doctor is giving lots of errors about unbrewed files:
>>>
>>> trevorkarn@Trevors-MacBook-Air sage % brew doctor
>>>
>>> *Please note that these warnings are just used to help the Homebrew 
>>> maintainers*
>>>
>>> *with debugging if you file an issue. If everything you use Homebrew for 
>>> is*
>>>
>>> *working fine: please don't worry or file an issue; just ignore this. 
>>> Thanks!*
>>>
>>>
>>> Warning: Unbrewed dylibs were found in /usr/local/lib.
>>>
>>> If you didn't put them there on purpose they could cause problems when
>>>
>>> building Homebrew formulae, and may need to be deleted.
>>>
>>>
>>> Unexpected dylibs:
>>>
>>>   /usr/local/lib/libtcl8.6.dylib
>>>
>>>   /usr/local/lib/libtk8.6.dylib
>>>
>>>
>>> Warning: Unbrewed header files were found in /usr/local/include.
>>>
>>> If you didn't put them there on purpose they could cause problems when
>>>
>>> building Homebrew formulae, and may need to be deleted.
>>>
>>>
>>> Unexpected header files:
>>>
>>>   /usr/local/include/fakemysql.h
>>>
>>>   /usr/local/include/fakepq.h
>>>
>>>   /usr/local/include/fakesql.h
>>>
>>>   /usr/local/include/itcl.h
>>>
>>>   /usr/local/include/itcl2TclOO.h
>>>
>>>   /usr/local/include/itclDecls.h
>>>
>>>   /usr/local/include/itclInt.h
>>>
>>>   /usr/local/include/itclIntDecls.h
>>>
>>>   /usr/local/include/itclMigrate2TclCore.h
>>>
>>>   /usr/local/include/itclTclIntStubsFcn.h
>>>
>>>   

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

es, 69.2MB)
>
> Removing: /usr/local/Cellar/libevent/2.1.11... (1,063 files, 5MB)
>
> Removing: /usr/local/Cellar/libffi/3.2.1... (16 files, 296.8KB)
>
> Removing: /usr/local/Cellar/libidn2/2.2.0_1... (70 files, 700.9KB)
>
> Removing: /usr/local/Cellar/libtasn1/4.14... (59 files, 384KB)
>
> Removing: /usr/local/Cellar/nettle/3.4.1... (85 files, 2MB)
>
> Error: Interrupted system call @ dir_initialize - /usr/local/Cellar/opus
>
> trevorkarn@Trevors-MacBook-Air sage % ;2D
>
> Best Regards,
>
> Trevor Karn
>
>
> On Mon, Feb 8, 2021 at 8:38 PM Zachary Scherr  wrote:
>
>> In your original config.log, it looked like sage was picking up its own 
>> fortran:
>>
>> configure:11991: gfortran has already been installed by SageMath
>> configure:39396: result: gfortran-9.2.0: 
>>  already installed as an SPKG
>>
>> The current version of gfortran from homebrew is 10.2.0 version 3
>>
>> GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
>> Copyright (C) 2020 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.  There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR 
>> PURPOSE.
>>
>> ./configure should be picking up homebrew's gfortran (installed with 
>> gcc), and it seems from your config.log file that you do have homebrew and 
>> therefore you should have the most recent gfortran.
>> Do you have the newest config.log file from after running make distclean? 
>> You may also want to try running
>>
>> brew doctor
>>
>> to see if there is something wrong with your homebrew. 
>> On Monday, February 8, 2021 at 9:27:11 PM UTC-5 Trevor Karn wrote:
>>
>>> Unfortunately, that did not seem to work. 
>>>
>>> Here are the last few lines of the terminal output and I've attached the 
>>> numpy log.
>>>
>>> [singular-4.1.1p2.p0] real 28m38.843s
>>>
>>> [singular-4.1.1p2.p0] user 24m18.545s
>>>
>>> [singular-4.1.1p2.p0] sys 3m53.423s
>>>
>>> [singular-4.1.1p2.p0] Copying package files from temporary location 
>>> /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/singular-4.1.1p2.p0/inst
>>>  
>>> to /Users/trevorkarn/Applications/sage/local
>>>
>>> [singular-4.1.1p2.p0] Successfully installed singular-4.1.1p2.p0
>>>
>>> [singular-4.1.1p2.p0] Deleting temporary build directory
>>>
>>> [singular-4.1.1p2.p0] 
>>> /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/singular-4.1.1p2.p0
>>>
>>> [singular-4.1.1p2.p0] Finished installing singular-4.1.1p2.p0
>>>
>>> make[2]: *** [all-build] Error 2
>>>
>>>
>>> real 182m14.796s
>>>
>>> user 355m33.883s
>>>
>>> sys 72m32.388s
>>>
>>> ***********
>>>
>>> Error building Sage.
>>>
>>>
>>> The following package(s) may have failed to build (not necessarily
>>>
>>> during this run of 'make all-build'):
>>>
>>>
>>> * package: numpy-1.19.4
>>>
>>>   last build time: Feb 8 19:48
>>>
>>>   log file:
>>> /Users/trevorkarn/Applications/sage/logs/pkgs/numpy-1.19.4.log
>>>
>>>   build directory: 
>>> /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/numpy-1.19.4
>>>
>>>
>>> It is safe to delete any log files and build directories, but they
>>>
>>> contain information that is helpful for debugging build problems.
>>>
>>> WARNING: If you now run 'make' again, the build directory of the
>>>
>>> same version of the package will, by default, be deleted. Set the
>>>
>>> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
>>>
>>>
>>> make[1]: *** [all-build] Error 1
>>>
>>> make: *** [build] Error 2
>>>
>>> trevorkarn@Trevors-MacBook-Air sage %
>>>
>>>
>>> Best Regards,
>>>
>>> Trevor Karn
>>>
>>>
>>> On Mon, Feb 8, 2021 at 1:56 PM Zachary Scherr  wrote:
>>>
>>>> yea, something seems messed up.  For example, the numpy problem was 
>>>> fixed on beta 6 and should still be fixed in beta 7.  It looks like 
>>>> somehow 
>>>> you have old files hanging around which are causing problems.  Hopefully 
>>>> make distclean will clean everyt

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

In your original config.log, it looked like sage was picking up its own 
fortran:

configure:11991: gfortran has already been installed by SageMath
configure:39396: result: gfortran-9.2.0: 
 already installed as an SPKG

The current version of gfortran from homebrew is 10.2.0 version 3

GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

./configure should be picking up homebrew's gfortran (installed with gcc), 
and it seems from your config.log file that you do have homebrew and 
therefore you should have the most recent gfortran.
Do you have the newest config.log file from after running make distclean? 
You may also want to try running

brew doctor

to see if there is something wrong with your homebrew. 
On Monday, February 8, 2021 at 9:27:11 PM UTC-5 Trevor Karn wrote:

> Unfortunately, that did not seem to work. 
>
> Here are the last few lines of the terminal output and I've attached the 
> numpy log.
>
> [singular-4.1.1p2.p0] real 28m38.843s
>
> [singular-4.1.1p2.p0] user 24m18.545s
>
> [singular-4.1.1p2.p0] sys 3m53.423s
>
> [singular-4.1.1p2.p0] Copying package files from temporary location 
> /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/singular-4.1.1p2.p0/inst
>  
> to /Users/trevorkarn/Applications/sage/local
>
> [singular-4.1.1p2.p0] Successfully installed singular-4.1.1p2.p0
>
> [singular-4.1.1p2.p0] Deleting temporary build directory
>
> [singular-4.1.1p2.p0] 
> /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/singular-4.1.1p2.p0
>
> [singular-4.1.1p2.p0] Finished installing singular-4.1.1p2.p0
>
> make[2]: *** [all-build] Error 2
>
>
> real 182m14.796s
>
> user 355m33.883s
>
> sys 72m32.388s
>
> ***
>
> Error building Sage.
>
>
> The following package(s) may have failed to build (not necessarily
>
> during this run of 'make all-build'):
>
>
> * package: numpy-1.19.4
>
>   last build time: Feb 8 19:48
>
>   log file:
> /Users/trevorkarn/Applications/sage/logs/pkgs/numpy-1.19.4.log
>
>   build directory: 
> /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/numpy-1.19.4
>
>
> It is safe to delete any log files and build directories, but they
>
> contain information that is helpful for debugging build problems.
>
> WARNING: If you now run 'make' again, the build directory of the
>
> same version of the package will, by default, be deleted. Set the
>
> environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
>
>
> make[1]: *** [all-build] Error 1
>
> make: *** [build] Error 2
>
> trevorkarn@Trevors-MacBook-Air sage %
>
>
> Best Regards,
>
> Trevor Karn
>
>
> On Mon, Feb 8, 2021 at 1:56 PM Zachary Scherr  wrote:
>
>> yea, something seems messed up.  For example, the numpy problem was fixed 
>> on beta 6 and should still be fixed in beta 7.  It looks like somehow you 
>> have old files hanging around which are causing problems.  Hopefully make 
>> distclean will clean everything and let you start fresh.
>>
>> On Monday, February 8, 2021 at 2:25:16 PM UTC-5 Trevor Karn wrote:
>>
>>> I must have typed it wrong. The second option you gave failed on numpy, 
>>> but I tried the first option again, and it is compiling.
>>>
>>> Best Regards,
>>>
>>> Trevor Karn
>>>
>>>
>>> On Mon, Feb 8, 2021 at 11:31 AM Zachary Scherr  wrote:
>>>
>>>> Are you sure you typed it correctly? Maybe try running
>>>>
>>>> ./bootstrap
>>>>
>>>> to make sure that the make targets are in order.
>>>>
>>>> On Monday, February 8, 2021 at 12:27:01 PM UTC-5 Trevor Karn wrote:
>>>>
>>>>> I tried make distclean and got an error “make: *** No rule to make 
>>>>> target ‘distclean’. Stop.”
>>>>>
>>>>> So I tried your second suggestion and it seems to be working so far, 
>>>>> but it is still compiling.
>>>>>
>>>>> On Mon, Feb 8, 2021 at 10:29 AM Zachary Scherr  
>>>>> wrote:
>>>>>
>>>>>> Probably the thing to try would be:
>>>>>>
>>>>>> make distclean
>>>>>>
>>>>>> and then you can build from scratch via:
>>>>>>
>>>>>> ./bootstrap
>>>>>> source .homebrew-bu

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

yea, something seems messed up.  For example, the numpy problem was fixed 
on beta 6 and should still be fixed in beta 7.  It looks like somehow you 
have old files hanging around which are causing problems.  Hopefully make 
distclean will clean everything and let you start fresh.

On Monday, February 8, 2021 at 2:25:16 PM UTC-5 Trevor Karn wrote:

> I must have typed it wrong. The second option you gave failed on numpy, 
> but I tried the first option again, and it is compiling.
>
> Best Regards,
>
> Trevor Karn
>
>
> On Mon, Feb 8, 2021 at 11:31 AM Zachary Scherr  wrote:
>
>> Are you sure you typed it correctly? Maybe try running
>>
>> ./bootstrap
>>
>> to make sure that the make targets are in order.
>>
>> On Monday, February 8, 2021 at 12:27:01 PM UTC-5 Trevor Karn wrote:
>>
>>> I tried make distclean and got an error “make: *** No rule to make 
>>> target ‘distclean’. Stop.”
>>>
>>> So I tried your second suggestion and it seems to be working so far, but 
>>> it is still compiling.
>>>
>>> On Mon, Feb 8, 2021 at 10:29 AM Zachary Scherr  wrote:
>>>
>>>> Probably the thing to try would be:
>>>>
>>>> make distclean
>>>>
>>>> and then you can build from scratch via:
>>>>
>>>> ./bootstrap
>>>> source .homebrew-build-env
>>>> ./configure
>>>> make -j4 build
>>>>
>>>> But if you want to try cleaning wheel first before starting from 
>>>> scratch, you could just try
>>>>
>>>> make wheel-clean
>>>> make -j4 build
>>>>
>>>> but it might be better to clean everything and start from scratch.
>>>>
>>>> On Monday, February 8, 2021 at 10:59:05 AM UTC-5 Trevor Karn wrote:
>>>>
>>>>> I do not see pep425tags.py in that directory. 
>>>>>
>>>>> trevorkarn@Trevors-MacBook-Air sage % cd 
>>>>> /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/
>>>>>
>>>>> trevorkarn@Trevors-MacBook-Air wheel % ls
>>>>>
>>>>> __init__.py __pycache__ cli metadata.py util.py wheelfile.py
>>>>>
>>>>> __main__.py bdist_wheel.py macosx_libfile.py pkginfo.py vendored
>>>>>
>>>>> Is there a way to clean the build environment?
>>>>>
>>>>> Best Regards,
>>>>>
>>>>> Trevor Karn
>>>>>
>>>>>
>>>>> On Mon, Feb 8, 2021 at 9:54 AM Dima Pasechnik  
>>>>> wrote:
>>>>>
>>>>>> the only explanation for pep425tags.py would be an unclean build
>>>>>> environment - e.g. weird env vars set, or strange stuff in PATH.
>>>>>>
>>>>>> On Mon, Feb 8, 2021 at 3:51 PM Zachary Scherr  
>>>>>> wrote:
>>>>>> >
>>>>>> > and do you see that pep425tags.py file in that directory?
>>>>>> >
>>>>>> > On Monday, February 8, 2021 at 10:21:09 AM UTC-5 Trevor Karn wrote:
>>>>>> >>
>>>>>> >> The only contents of the file you pointed me towards are
>>>>>> >>
>>>>>> >> __version__ = '0.36.2'
>>>>>> >>
>>>>>> >> Best Regards,
>>>>>> >>
>>>>>> >> Trevor Karn
>>>>>> >>
>>>>>> >>
>>>>>> >> On Mon, Feb 8, 2021 at 9:09 AM Zachary Scherr  
>>>>>> wrote:
>>>>>> >>>
>>>>>> >>> I really don't understand.  The Cython log file shows that the 
>>>>>> problem is in
>>>>>> >>>
>>>>>> >>> 
>>>>>> /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/pep425tags.py
>>>>>> >>>
>>>>>> >>> I could be mistaken, but I don't think pep425tags.py has been a 
>>>>>> part of the wheel package for a while now.  Certainly when I looked at 
>>>>>> wheel on my sage there was no such file.
>>>>>> >>>
>>>>>> >>> Can you go to your 
>>>>>> "/Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/"
>>>>>>  
>>>>>> directory and take a look at __init__.py.  Does

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

Are you sure you typed it correctly? Maybe try running

./bootstrap

to make sure that the make targets are in order.

On Monday, February 8, 2021 at 12:27:01 PM UTC-5 Trevor Karn wrote:

> I tried make distclean and got an error “make: *** No rule to make target 
> ‘distclean’. Stop.”
>
> So I tried your second suggestion and it seems to be working so far, but 
> it is still compiling.
>
> On Mon, Feb 8, 2021 at 10:29 AM Zachary Scherr  wrote:
>
>> Probably the thing to try would be:
>>
>> make distclean
>>
>> and then you can build from scratch via:
>>
>> ./bootstrap
>> source .homebrew-build-env
>> ./configure
>> make -j4 build
>>
>> But if you want to try cleaning wheel first before starting from scratch, 
>> you could just try
>>
>> make wheel-clean
>> make -j4 build
>>
>> but it might be better to clean everything and start from scratch.
>>
>> On Monday, February 8, 2021 at 10:59:05 AM UTC-5 Trevor Karn wrote:
>>
>>> I do not see pep425tags.py in that directory. 
>>>
>>> trevorkarn@Trevors-MacBook-Air sage % cd 
>>> /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/
>>>
>>> trevorkarn@Trevors-MacBook-Air wheel % ls
>>>
>>> __init__.py __pycache__ cli metadata.py util.py wheelfile.py
>>>
>>> __main__.py bdist_wheel.py macosx_libfile.py pkginfo.py vendored
>>>
>>> Is there a way to clean the build environment?
>>>
>>> Best Regards,
>>>
>>> Trevor Karn
>>>
>>>
>>> On Mon, Feb 8, 2021 at 9:54 AM Dima Pasechnik  wrote:
>>>
>>>> the only explanation for pep425tags.py would be an unclean build
>>>> environment - e.g. weird env vars set, or strange stuff in PATH.
>>>>
>>>> On Mon, Feb 8, 2021 at 3:51 PM Zachary Scherr  wrote:
>>>> >
>>>> > and do you see that pep425tags.py file in that directory?
>>>> >
>>>> > On Monday, February 8, 2021 at 10:21:09 AM UTC-5 Trevor Karn wrote:
>>>> >>
>>>> >> The only contents of the file you pointed me towards are
>>>> >>
>>>> >> __version__ = '0.36.2'
>>>> >>
>>>> >> Best Regards,
>>>> >>
>>>> >> Trevor Karn
>>>> >>
>>>> >>
>>>> >> On Mon, Feb 8, 2021 at 9:09 AM Zachary Scherr  
>>>> wrote:
>>>> >>>
>>>> >>> I really don't understand.  The Cython log file shows that the 
>>>> problem is in
>>>> >>>
>>>> >>> 
>>>> /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/pep425tags.py
>>>> >>>
>>>> >>> I could be mistaken, but I don't think pep425tags.py has been a 
>>>> part of the wheel package for a while now.  Certainly when I looked at 
>>>> wheel on my sage there was no such file.
>>>> >>>
>>>> >>> Can you go to your 
>>>> "/Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/"
>>>>  
>>>> directory and take a look at __init__.py.  Does the version say 0.36.2?
>>>> >>>
>>>> >>> On Monday, February 8, 2021 at 9:32:20 AM UTC-5 Trevor Karn wrote:
>>>> >>>>
>>>> >>>>
>>>> >>>> Here is what I get. It seems like it is the same as yours?
>>>> >>>>
>>>> >>>>
>>>> >>>> trevorkarn@Trevors-MacBook-Air sage % brew info python3
>>>> >>>>
>>>> >>>> python@3.9: stable 3.9.1
>>>> >>>>
>>>> >>>> Interpreted, interactive, object-oriented programming language
>>>> >>>>
>>>> >>>> https://www.python.org/
>>>> >>>>
>>>> >>>> /usr/local/Cellar/python@3.9/3.9.1_8 (8,665 files, 129.4MB) *
>>>> >>>>
>>>> >>>>   Built from source on 2021-02-05 at 16:39:31
>>>> >>>>
>>>> >>>> From: 
>>>> https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb
>>>> >>>>
>>>> >>>> License: Python-2.0
>>>> >>>>
>>>> >>>> ==> Dependencies
>>>> >>

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

Probably the thing to try would be:

make distclean

and then you can build from scratch via:

./bootstrap
source .homebrew-build-env
./configure
make -j4 build

But if you want to try cleaning wheel first before starting from scratch, 
you could just try

make wheel-clean
make -j4 build

but it might be better to clean everything and start from scratch.

On Monday, February 8, 2021 at 10:59:05 AM UTC-5 Trevor Karn wrote:

> I do not see pep425tags.py in that directory. 
>
> trevorkarn@Trevors-MacBook-Air sage % cd 
> /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/
>
> trevorkarn@Trevors-MacBook-Air wheel % ls
>
> __init__.py __pycache__ cli metadata.py util.py wheelfile.py
>
> __main__.py bdist_wheel.py macosx_libfile.py pkginfo.py vendored
>
> Is there a way to clean the build environment?
>
> Best Regards,
>
> Trevor Karn
>
>
> On Mon, Feb 8, 2021 at 9:54 AM Dima Pasechnik  wrote:
>
>> the only explanation for pep425tags.py would be an unclean build
>> environment - e.g. weird env vars set, or strange stuff in PATH.
>>
>> On Mon, Feb 8, 2021 at 3:51 PM Zachary Scherr  wrote:
>> >
>> > and do you see that pep425tags.py file in that directory?
>> >
>> > On Monday, February 8, 2021 at 10:21:09 AM UTC-5 Trevor Karn wrote:
>> >>
>> >> The only contents of the file you pointed me towards are
>> >>
>> >> __version__ = '0.36.2'
>> >>
>> >> Best Regards,
>> >>
>> >> Trevor Karn
>> >>
>> >>
>> >> On Mon, Feb 8, 2021 at 9:09 AM Zachary Scherr  
>> wrote:
>> >>>
>> >>> I really don't understand.  The Cython log file shows that the 
>> problem is in
>> >>>
>> >>> 
>> /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/pep425tags.py
>> >>>
>> >>> I could be mistaken, but I don't think pep425tags.py has been a part 
>> of the wheel package for a while now.  Certainly when I looked at wheel on 
>> my sage there was no such file.
>> >>>
>> >>> Can you go to your 
>> "/Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/"
>>  
>> directory and take a look at __init__.py.  Does the version say 0.36.2?
>> >>>
>> >>> On Monday, February 8, 2021 at 9:32:20 AM UTC-5 Trevor Karn wrote:
>> >>>>
>> >>>>
>> >>>> Here is what I get. It seems like it is the same as yours?
>> >>>>
>> >>>>
>> >>>> trevorkarn@Trevors-MacBook-Air sage % brew info python3
>> >>>>
>> >>>> python@3.9: stable 3.9.1
>> >>>>
>> >>>> Interpreted, interactive, object-oriented programming language
>> >>>>
>> >>>> https://www.python.org/
>> >>>>
>> >>>> /usr/local/Cellar/python@3.9/3.9.1_8 (8,665 files, 129.4MB) *
>> >>>>
>> >>>>   Built from source on 2021-02-05 at 16:39:31
>> >>>>
>> >>>> From: 
>> https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb
>> >>>>
>> >>>> License: Python-2.0
>> >>>>
>> >>>> ==> Dependencies
>> >>>>
>> >>>> Build: pkg-config ✔
>> >>>>
>> >>>> Required: gdbm ✔, openssl@1.1 ✔, readline ✔, sqlite ✔, tcl-tk ✔, xz ✔
>> >>>>
>> >>>> ==> Caveats
>> >>>>
>> >>>> Python has been installed as
>> >>>>
>> >>>>   /usr/local/bin/python3
>> >>>>
>> >>>>
>> >>>> Unversioned symlinks `python`, `python-config`, `pip` etc. pointing 
>> to
>> >>>>
>> >>>> `python3`, `python3-config`, `pip3` etc., respectively, have been 
>> installed into
>> >>>>
>> >>>>   /usr/local/opt/python@3.9/libexec/bin
>> >>>>
>> >>>>
>> >>>> You can install Python packages with
>> >>>>
>> >>>>   pip3 install 
>> >>>>
>> >>>> They will install into the site-package directory
>> >>>>
>> >>>>   /usr/local/lib/python3.9/site-packages
>> >>>>
>> >>>>
>> >>>> See

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

and do you see that pep425tags.py file in that directory?

On Monday, February 8, 2021 at 10:21:09 AM UTC-5 Trevor Karn wrote:

> The only contents of the file you pointed me towards are
>
> __version__ = '0.36.2'
>
> Best Regards,
>
> Trevor Karn
>
>
> On Mon, Feb 8, 2021 at 9:09 AM Zachary Scherr  wrote:
>
>> I really don't understand.  The Cython log file shows that the problem is 
>> in
>>
>>
>> /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/pep425tags.py
>>
>> I could be mistaken, but I don't think pep425tags.py has been a part of 
>> the wheel package for a while now.  Certainly when I looked at wheel on my 
>> sage there was no such file.
>>
>> Can you go to your 
>> "/Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/"
>>  
>> directory and take a look at __init__.py.  Does the version say 0.36.2?
>>
>> On Monday, February 8, 2021 at 9:32:20 AM UTC-5 Trevor Karn wrote:
>>
>>>
>>> Here is what I get. It seems like it is the same as yours?
>>>
>>>
>>> trevorkarn@Trevors-MacBook-Air sage % brew info python3
>>>
>>> python@3.9: stable 3.9.1
>>>
>>> Interpreted, interactive, object-oriented programming language
>>>
>>> https://www.python.org/
>>>
>>> /usr/local/Cellar/python@3.9/3.9.1_8 (8,665 files, 129.4MB) *
>>>
>>>   Built from source on 2021-02-05 at 16:39:31
>>>
>>> From: 
>>> https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb 
>>> <https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb>
>>>
>>> License: Python-2.0
>>>
>>> ==> *Dependencies*
>>>
>>> Build: *pkg-config **✔*
>>>
>>> Required: *gdbm **✔*, *openssl@1.1 **✔*, *readline **✔*, *sqlite **✔*, 
>>> *tcl-tk 
>>> **✔*, *xz **✔*
>>>
>>> ==> *Caveats*
>>>
>>> Python has been installed as
>>>
>>>   /usr/local/bin/python3
>>>
>>>
>>> Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
>>>
>>> `python3`, `python3-config`, `pip3` etc., respectively, have been 
>>> installed into
>>>
>>>   /usr/local/opt/python@3.9/libexec/bin
>>>
>>>
>>> You can install Python packages with
>>>
>>>   pip3 install 
>>>
>>> They will install into the site-package directory
>>>
>>>   /usr/local/lib/python3.9/site-packages
>>>
>>>
>>> See: https://docs.brew.sh/Homebrew-and-Python
>>>
>>> ==> *Analytics*
>>>
>>> install: 755,419 (30 days), 2,396,024 (90 days), 2,995,387 (365 days)
>>>
>>> install-on-request: 244,063 (30 days), 714,665 (90 days), 799,812 (365 
>>> days)
>>>
>>> build-error: 0 (30 days)
>>>
>>> Best Regards,
>>>
>>> Trevor Karn
>>>
>>>
>>> On Mon, Feb 8, 2021 at 8:17 AM Dima Pasechnik  wrote:
>>>
>>>> Could it be that you need to update your Homebrew (?) python3 package?
>>>> What version do you have now?
>>>> E.g. on a box where the latest Sage builds I have
>>>>
>>>> % brew info python3
>>>>
>>>> python@3.9: stable 3.9.1 (bottled)
>>>> Interpreted, interactive, object-oriented programming language
>>>> https://www.python.org/
>>>> /usr/local/Cellar/python@3.9/3.9.1_8 (4,057 files, 67.8MB) *
>>>>   Poured from bottle on 2021-02-06 at 10:13:24
>>>> From: 
>>>> https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb 
>>>> <https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb>
>>>>
>>>>
>>>> On Mon, Feb 8, 2021 at 1:53 PM Trevor Karn  wrote:
>>>> >
>>>> > Ah I see, thanks for explaining.
>>>> >
>>>> > Here is my top-level config.log.
>>>> >
>>>> > Best Regards,
>>>> >
>>>> > Trevor Karn
>>>> >
>>>> >
>>>> > On Mon, Feb 8, 2021 at 7:09 AM Dima Pasechnik  
>>>> wrote:
>>>> >>
>>>> >>
>>>> >>
>>>> >> On Mon, 8 Feb 2021, 13:02 Trevor Karn,  wrote:
>>>> >>>
>>>> >>> Thanks for sending that link. I am confus

Re: [sage-devel] Trouble building cython

[Zachary Scherr]

I really don't understand.  The Cython log file shows that the problem is in

/Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/pep425tags.py

I could be mistaken, but I don't think pep425tags.py has been a part of the 
wheel package for a while now.  Certainly when I looked at wheel on my sage 
there was no such file.

Can you go to your 
"/Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/" 
directory and take a look at __init__.py.  Does the version say 0.36.2?

On Monday, February 8, 2021 at 9:32:20 AM UTC-5 Trevor Karn wrote:

>
> Here is what I get. It seems like it is the same as yours?
>
>
> trevorkarn@Trevors-MacBook-Air sage % brew info python3
>
> python@3.9: stable 3.9.1
>
> Interpreted, interactive, object-oriented programming language
>
> https://www.python.org/
>
> /usr/local/Cellar/python@3.9/3.9.1_8 (8,665 files, 129.4MB) *
>
>   Built from source on 2021-02-05 at 16:39:31
>
> From: 
> https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb 
> 
>
> License: Python-2.0
>
> ==> *Dependencies*
>
> Build: *pkg-config **✔*
>
> Required: *gdbm **✔*, *openssl@1.1 **✔*, *readline **✔*, *sqlite **✔*, 
> *tcl-tk 
> **✔*, *xz **✔*
>
> ==> *Caveats*
>
> Python has been installed as
>
>   /usr/local/bin/python3
>
>
> Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
>
> `python3`, `python3-config`, `pip3` etc., respectively, have been 
> installed into
>
>   /usr/local/opt/python@3.9/libexec/bin
>
>
> You can install Python packages with
>
>   pip3 install 
>
> They will install into the site-package directory
>
>   /usr/local/lib/python3.9/site-packages
>
>
> See: https://docs.brew.sh/Homebrew-and-Python
>
> ==> *Analytics*
>
> install: 755,419 (30 days), 2,396,024 (90 days), 2,995,387 (365 days)
>
> install-on-request: 244,063 (30 days), 714,665 (90 days), 799,812 (365 
> days)
>
> build-error: 0 (30 days)
>
> Best Regards,
>
> Trevor Karn
>
>
> On Mon, Feb 8, 2021 at 8:17 AM Dima Pasechnik  wrote:
>
>> Could it be that you need to update your Homebrew (?) python3 package?
>> What version do you have now?
>> E.g. on a box where the latest Sage builds I have
>>
>> % brew info python3
>>
>> python@3.9: stable 3.9.1 (bottled)
>> Interpreted, interactive, object-oriented programming language
>> https://www.python.org/
>> /usr/local/Cellar/python@3.9/3.9.1_8 (4,057 files, 67.8MB) *
>>   Poured from bottle on 2021-02-06 at 10:13:24
>> From: 
>> https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/pyt...@3.9.rb 
>> 
>>
>>
>> On Mon, Feb 8, 2021 at 1:53 PM Trevor Karn  wrote:
>> >
>> > Ah I see, thanks for explaining.
>> >
>> > Here is my top-level config.log.
>> >
>> > Best Regards,
>> >
>> > Trevor Karn
>> >
>> >
>> > On Mon, Feb 8, 2021 at 7:09 AM Dima Pasechnik  wrote:
>> >>
>> >>
>> >>
>> >> On Mon, 8 Feb 2021, 13:02 Trevor Karn,  wrote:
>> >>>
>> >>> Thanks for sending that link. I am confused though, because it says a 
>> fix was issued. Does that mean it should work now?
>> >>
>> >>
>> >> sorry, I was not clear. What I meant to say that it appears to be a 
>> well-known issue in the Python@macOS universe,
>> >> and lately all seems to be OK with Sage.
>> >>
>> >> To figure out exactly goes wrong in your case, we need to know where 
>> Python3 used in Sage is coming from.
>> >> Please post the top-level config.log
>> >>
>> >>
>> >>>
>> >>> And yes, I am on the most recent develop branch
>> >>>
>> >>> On Mon, Feb 8, 2021 at 5:42 AM Dima Pasechnik  
>> wrote:
>> 
>>  This seems to be well-known issue, see e.g
>>  https://github.com/pypa/virtualenv/issues/2027
>> 
>>  Are you on the most recent develop branch (9.3.beta7)?
>> 
>>  On Mon, Feb 8, 2021 at 9:20 AM Trevor Karn  
>> wrote:
>>  >
>>  > Hi,
>>  >
>>  > I'm trying to build Sage from the source code. I cloned it from 
>> git, and tried to build from the develop branch using make from the sage 
>> directory. I ran into trouble building cython. The error message suggested 
>> that I email this group. Does anyone have any advice on how to proceed?
>>  >
>>  > I am using macOS Big Sur 11.2 on a MacBook Air.
>>  >
>>  > The log file is attached, this is from a second run - it failed 
>> once, and I tried running make a second time without any changes and this 
>> is the log from the second run, which returns the same error just without 
>> all of the info before it (eg. the flint installation).
>>  >
>>  > Thanks so much.
>>  >
>>  > Best,
>>  > Trevor
>>  >
>>  > --
>>  > 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.
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Re: [sage-devel] Re: Problems with 9.3.beta6 + OS X Big Sur

[Zachary Scherr]

I found something possibly relevant at

https://bugs.python.org/issue42691

although there the complaint was that Homebrew built python against system 
tcl and the suggestion was that Homebrew use its own tcl-tk.  It seems that 
Homebrew is correctly using its own tcl-tk
since the line

5   libtcl8.6.dylib 0x00032998c72e AtForkPrepare + 
38

says that python is using tcl 8.6 and system tcl is 8.5.  No idea what's 
going on, but it might be good to try to produce a minimal reproducible 
example to show to the python/tcl people.
On Wednesday, February 3, 2021 at 12:11:54 PM UTC-5 dim...@gmail.com wrote:

>
>
> On Wed, 3 Feb 2021, 17:03 John H Palmieri,  wrote:
>
>> Right, thank you. Python 3.9 builds successfully.
>>
>> On Monday, February 1, 2021 at 7:14:29 PM UTC-8 zsc...@gmail.com wrote:
>>
>>> For the --with-system-python3=no, I don't know what the problem is but I 
>>> think it was fixed by upgrading to python 3.9 in 
>>> https://trac.sagemath.org/ticket/30589
>>>
>>> On Monday, February 1, 2021 at 9:45:37 PM UTC-5 John H Palmieri wrote:
>>>
 On OS X Big Sur (intel), as of the most recent Xcode and homebrew, I am 
 currently unable to build Sage with either homebrew's Python or with 
 `./configure --with-system-python3=no`.

 - With homebrew's Python, actually Sage builds but the documentation 
 does not (similar problems on both Big Sur and Catalina), ending with
>>>
>>>
> yes, I see this too. (with latest Homebrew python 3.9.)
>
> What exactly is broken there?
>
>
>

 
 0   signals.cpython-39-darwin.so0x00010cd40542 
 print_backtrace + 66
 1   signals.cpython-39-darwin.so0x00010cd44167 sigdie + 39
 2   signals.cpython-39-darwin.so0x00010cd4406a 
 cysigs_signal_handler + 282
 3   libsystem_platform.dylib0x7fff203bcd7d _sigtramp + 
 29
 4   ??? 0x003f 0x0 + 63
 5   libtcl8.6.dylib 0x00032998c72e 
 AtForkPrepare + 38
 6   libsystem_pthread.dylib 0x7fff203781a3 
 _pthread_atfork_prepare_handlers + 90
 7   libSystem.B.dylib   0x7fff2a575934 
 libSystem_atfork_prepare + 11
 8   libsystem_c.dylib   0x7fff2025bb1b fork + 12
 9   _posixsubprocess.cpython-39-darwin. 0x00010b63db89 
 subprocess_fork_exec + 1573
 10  Python  0x00010af10904 
 cfunction_call + 127
 11  Python  0x00010aedffa3 
 _PyObject_MakeTpCall + 266
 12  Python  0x00010af88027 
 call_function + 455
 ...
 157 Python  0x00010afcf10f Py_BytesMain 
 + 42
 158 libdyld.dylib   0x7fff20393621 start + 1
 
 Unhandled SIGILL: An illegal instruction occurred.
 This probably occurred because a *compiled* module has a bug
 in it and is not properly wrapped with sig_on(), sig_off().
 Python will now terminate.
 
 ...
   File 
 "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
  
 line 221, in reap_workers
 w = bring_out_yer_dead(w, task, exitcode)
   File 
 "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
  
 line 157, in bring_out_yer_dead
 raise WorkerDiedException(
 sage_setup.docbuild.utils.WorkerDiedException: worker for 
 ('reference/misc', 'en', 'html', {}) died with non-zero exit code -4

 - With `./configure --with-system-python3=no`, Python fails to build 
 (on Big Sur only; it succeeds on Catalina), saying

 ModuleNotFoundError: No module named 'readline'

 and

 ModuleNotFoundError: No module named 'zlib'

 Any suggestions?

 -- 
 John


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>>  
>> 
>> .
>>
>

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[sage-devel] Re: Problems with 9.3.beta6 + OS X Big Sur

[Zachary Scherr]

For the --with-system-python3=no, I don't know what the problem is but I 
think it was fixed by upgrading to python 3.9 
in https://trac.sagemath.org/ticket/30589

On Monday, February 1, 2021 at 9:45:37 PM UTC-5 John H Palmieri wrote:

> On OS X Big Sur (intel), as of the most recent Xcode and homebrew, I am 
> currently unable to build Sage with either homebrew's Python or with 
> `./configure --with-system-python3=no`.
>
> - With homebrew's Python, actually Sage builds but the documentation does 
> not (similar problems on both Big Sur and Catalina), ending with
>
> 
> 0   signals.cpython-39-darwin.so0x00010cd40542 
> print_backtrace + 66
> 1   signals.cpython-39-darwin.so0x00010cd44167 sigdie + 39
> 2   signals.cpython-39-darwin.so0x00010cd4406a 
> cysigs_signal_handler + 282
> 3   libsystem_platform.dylib0x7fff203bcd7d _sigtramp + 29
> 4   ??? 0x003f 0x0 + 63
> 5   libtcl8.6.dylib 0x00032998c72e AtForkPrepare + 
> 38
> 6   libsystem_pthread.dylib 0x7fff203781a3 
> _pthread_atfork_prepare_handlers + 90
> 7   libSystem.B.dylib   0x7fff2a575934 
> libSystem_atfork_prepare + 11
> 8   libsystem_c.dylib   0x7fff2025bb1b fork + 12
> 9   _posixsubprocess.cpython-39-darwin. 0x00010b63db89 
> subprocess_fork_exec + 1573
> 10  Python  0x00010af10904 cfunction_call 
> + 127
> 11  Python  0x00010aedffa3 
> _PyObject_MakeTpCall + 266
> 12  Python  0x00010af88027 call_function + 
> 455
> ...
> 157 Python  0x00010afcf10f Py_BytesMain + 
> 42
> 158 libdyld.dylib   0x7fff20393621 start + 1
> 
> Unhandled SIGILL: An illegal instruction occurred.
> This probably occurred because a *compiled* module has a bug
> in it and is not properly wrapped with sig_on(), sig_off().
> Python will now terminate.
> 
> ...
>   File 
> "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
>  
> line 221, in reap_workers
> w = bring_out_yer_dead(w, task, exitcode)
>   File 
> "/Users/palmieri/Desktop/Sage/sage_builds/TESTING/sage-9.3.beta6/local/lib/python3.9/site-packages/sage_setup/docbuild/utils.py",
>  
> line 157, in bring_out_yer_dead
> raise WorkerDiedException(
> sage_setup.docbuild.utils.WorkerDiedException: worker for 
> ('reference/misc', 'en', 'html', {}) died with non-zero exit code -4
>
> - With `./configure --with-system-python3=no`, Python fails to build (on 
> Big Sur only; it succeeds on Catalina), saying
>
> ModuleNotFoundError: No module named 'readline'
>
> and
>
> ModuleNotFoundError: No module named 'zlib'
>
> Any suggestions?
>
> -- 
> John
>
>
>

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[sage-devel] Re: SSL missing

[Zachary Scherr]

Actually, it looks like you don't already need SSL installed since it comes 
with that fix.

On Monday, January 25, 2021 at 7:10:25 PM UTC-5 Zachary Scherr wrote:

>
> If you have SSL installed, say through homebrew, then you can use the 
> following script: https://github.com/3-manifolds/fix_mac_sage
> On Monday, January 25, 2021 at 7:06:08 PM UTC-5 pols...@gmail.com wrote:
>
>> Dear developers of SageMath,
>>
>> I keep encountering this error (see log attached) with any binary install 
>> in my work macOS Big Sur system (11.1) - I’ve tried as an app and simply 
>> unpacking the compressed file to launch from the terminal. I’ve installed 
>> openssl with brew (brew install openssl) and tried to launch “sage -f 
>> python3” as instructed, but it failed.
>>
>> I would be most happy to help debug this in case it’s not an isolated 
>> case. Otherwise, I’d appreciate some pointers on how to fix this.
>>
>> Thank you kindly.
>>
>> BR,
>>
>> /Pol
>>
>

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[sage-devel] Re: SSL missing

[Zachary Scherr]

If you have SSL installed, say through homebrew, then you can use the 
following script: https://github.com/3-manifolds/fix_mac_sage
On Monday, January 25, 2021 at 7:06:08 PM UTC-5 pols...@gmail.com wrote:

> Dear developers of SageMath,
>
> I keep encountering this error (see log attached) with any binary install 
> in my work macOS Big Sur system (11.1) - I’ve tried as an app and simply 
> unpacking the compressed file to launch from the terminal. I’ve installed 
> openssl with brew (brew install openssl) and tried to launch “sage -f 
> python3” as instructed, but it failed.
>
> I would be most happy to help debug this in case it’s not an isolated 
> case. Otherwise, I’d appreciate some pointers on how to fix this.
>
> Thank you kindly.
>
> BR,
>
> /Pol
>

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[sage-devel] Re: Unable to build develop branch

[Zachary Scherr]

#31166 is already merged into the latest develop branch so you shouldn't 
have to merge that.  Scipy should build with #31183 so maybe try again and 
post the log file.  If you need scipy to build you can also do:

MACOSX_DEPLOYMENT_TARGET=11.0 make scipy

which should fix the problem you are seeing.

On Friday, January 22, 2021 at 2:30:57 PM UTC-5 dwb...@gmail.com wrote:

> Thanks!
>
> But it didn't fix it for me. For me the u/jhpalmieri/scipy-big-sur 
> 
>  fails 
> in numpy and
> doesn't get to scipy. So I merged the change in #31166 (addressing numpy) 
> into
> the scipy-big-sur branch and that fails to build in scipy again.
>
> Dan
>
> On Thursday, January 21, 2021 at 8:09:14 PM UTC-8 John H Palmieri wrote:
>
>> Ticket 31183 (https://trac.sagemath.org/ticket/31183) should fix that. 
>> Merging that into the develop branch works for me.
>>
>> -- 
>> John
>>
>>
>> On Thursday, January 21, 2021 at 8:03:55 PM UTC-8 dwb...@gmail.com wrote:
>>
>>> I'm unable to build the develop branch since upgrading my iMac to Big 
>>> Sur. I have python3 and scipy installed through homebrew. In /usr/local/bin 
>>> I have a symbolic link from python to python3.
>>>
>>> Although I have scipy through homebrew, Sage insists on installing the 
>>> spkg. In previous build attempts (in late December) the build failed in 
>>> numpy.
>>>
>>> I'm attaching my scipy.1.5.4.log. I would appreciate any suggestions.
>>>
>>> Thank you,
>>> Daniel Bump
>>>
>>>
>>>

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Re: [sage-devel] Help with installing package lrslib-062+autotools-2017-03-03.p1

[Zachary Scherr]

Did you build sage from source? I had success getting lrslib to build by 
running:

CFLAGS=-Wno-implicit-function-declaration make lrslib

if you didn't build from source then you might try

CFLAGS=-Wno-implicit-function-declaration sage -i lrslib

On Thursday, January 14, 2021 at 2:01:36 PM UTC-5, Lisa Marie wrote:
>
> Hi,
>
> thanks for the quick help.
>
> I'm not really familiar with compiler flags. Could you specify your answer 
> a bit? Would be really helpful for me!
>
> Regards, Lisa
>
> dim...@gmail.com schrieb am Donnerstag, 14. Januar 2021 um 17:38:17 UTC+1:
>
>> the problem is that the compiler in XCode 12 has unreasonable assumptions 
>> about C/C++ code.
>> This most probably can be fixed by setting appropriate compiler flags. 
>> See the relevant to XCode   12 and macOS 11 tickets on trac.sagemath.org
>>
>>
>>
>> On Thu, 14 Jan 2021, 15:38 Lisa Marie,  wrote:
>>
>>> Hey everybody,
>>>
>>> I have a problem with installing the 
>>> package lrslib-062+autotools-2017-03-03.p1 for sage. I work on an Macbook 
>>> with an Intelprocessor and MacOSX Big Sur, 11.1. I also installed every 
>>> package recommended for sage. 
>>>
>>> Can you help me fix the problem or at least say what the problem is?
>>>
>>> The log-file of the problem is appended.
>>>
>>> Thanks for helping!
>>> Lisa
>>>
>>> -- 
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>>>  
>>> 
>>> .
>>>
>>

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Re: [sage-devel] Purpose of SAGE_MACOSX_DEPLOYMENT_TARGET

[Zachary Scherr]

That's a fair point.  I guess it's a bit more relevant at the moment since 
homebrew python is, at least for the time being, no longer suitable and 
system python3 is only 3.8.  So for people who have homebrew python 
installed they can't get python 3.9 in sage 9.3 unless they build from 
source.

In any case, it seems prudent to try to figure out what's going on with 
MACOSX_DEPLOYMENT_TARGET.  I'll try to investigate to the best of my 
ability, but I wonder if the problems that led to setting it to 10.9 ten 
years ago are still relevant today.

On Thursday, January 14, 2021 at 4:44:09 AM UTC-5, Dima Pasechnik wrote:
>
>
>
> On Thu, 14 Jan 2021, 00:52 Zachary Scherr, > 
> wrote:
>
>> I've been trying to help out with getting sage to work properly on Mac, 
>> and I was curious if anyone can explain the purpose of 
>> SAGE_MACOSX_DEPLOYMENT_TARGET to me.
>>
>> I don't know autoconf at all, but I find that if I configure with 
>> --with-system-python3=no
>> then SAGE_MACOSX_DEPLOYMENT_TARGET gets set to "legacy".  This is 
>> presumably because of the lines
>>
>> AS_IF([test x$sage_spkg_install_python3 = xno],
>>   [PYTHON_FOR_VENV="$ac_cv_path_PYTHON3"],
>>   [SAGE_MACOSX_DEPLOYMENT_TARGET=legacy])
>> AC_SUBST([PYTHON_FOR_VENV])
>> AC_SUBST([SAGE_MACOSX_DEPLOYMENT_TARGET])
>>
>> located in build/pkgs/python3/spkg-configure.m4.
>>
>> As far as I can tell, this leads to all sorts of warnings when doctesting 
>> sage. 
>>
>
> I would treat the very idea of not using an already installed python3 as a 
> legacy option.
>
> But yes, the issue is related to the correct setting of 
> MACOSX_DEPLOYMENT_TARGET 
> - something that only Apple itself understands well :-)
>
>
> Specifically, I get lots of warnings like:
>>
>> ld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer 
>> macOS version (10.15) than being linked (10.9)
>> ld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer 
>> macOS version (10.15) than being linked (10.9)
>> ld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for 
>> newer macOS version (10.15) than being linked (10.9)
>> ld: warning: dylib (/usr/local/lib/libgsl.dylib) was built for newer 
>> macOS version (10.15) than being linked (10.9)
>> ld: warning: dylib (/usr/local/lib/libntl.dylib) was built for newer 
>> macOS version (10.15) than being linked (10.9)
>>
>> now I believe that this is caused by src/bin/sage-env which has the 
>> following code:
>>
>> if [ "$UNAME" = "Darwin" ]; then
>>   export MACOSX_VERSION=`uname -r | awk -F. '{print $1}'`
>>   case "$SAGE_MACOSX_DEPLOYMENT_TARGET" in
>>   legacy)
>> # legacy behavior of the Sage distribution.
>> # set MACOSX_DEPLOYMENT_TARGET -- if set incorrectly, this can
>> # cause lots of random "Abort trap" issues on OSX. see trac
>> # #7095 for an example.
>> if [ $MACOSX_VERSION -ge 14 ]; then
>> # various packages have still have issues with
>> # two digit OS X versions
>> MACOSX_DEPLOYMENT_TARGET=10.9
>> else
>> MACOSX_DEPLOYMENT_TARGET=10.$[$MACOSX_VERSION-4]
>> fi
>> export MACOSX_DEPLOYMENT_TARGET
>> ;;
>>   "")
>> # Do nothing
>> ;;
>>   *)
>> # A fixed version set at configure time.
>> export MACOSX_DEPLOYMENT_TARGET=$SAGE_MACOSX_DEPLOYMENT_TARGET
>> ;;
>>   esac
>>
>> and I'm trying to understand where all of this is coming from.  The trac 
>> ticket this references is 11 years old and so I'm not sure it's an issue 
>> any more.
>>
>> -- 
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>> "sage-devel" group.
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>> email to sage-...@googlegroups.com .
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>> https://groups.google.com/d/msgid/sage-devel/19afd68d-be22-4a98-a3e7-c694fc6135a8n%40googlegroups.com
>>  
>> <https://groups.google.com/d/msgid/sage-devel/19afd68d-be22-4a98-a3e7-c694fc6135a8n%40googlegroups.com?utm_medium=email_source=footer>
>> .
>>
>

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[sage-devel] Purpose of SAGE_MACOSX_DEPLOYMENT_TARGET

[Zachary Scherr]

I've been trying to help out with getting sage to work properly on Mac, and 
I was curious if anyone can explain the purpose of 
SAGE_MACOSX_DEPLOYMENT_TARGET to me.

I don't know autoconf at all, but I find that if I configure with 
--with-system-python3=no
then SAGE_MACOSX_DEPLOYMENT_TARGET gets set to "legacy".  This is 
presumably because of the lines

AS_IF([test x$sage_spkg_install_python3 = xno],
  [PYTHON_FOR_VENV="$ac_cv_path_PYTHON3"],
  [SAGE_MACOSX_DEPLOYMENT_TARGET=legacy])
AC_SUBST([PYTHON_FOR_VENV])
AC_SUBST([SAGE_MACOSX_DEPLOYMENT_TARGET])

located in build/pkgs/python3/spkg-configure.m4.

As far as I can tell, this leads to all sorts of warnings when doctesting 
sage.  Specifically, I get lots of warnings like:

ld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer 
macOS version (10.15) than being linked (10.9)
ld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer 
macOS version (10.15) than being linked (10.9)
ld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for newer 
macOS version (10.15) than being linked (10.9)
ld: warning: dylib (/usr/local/lib/libgsl.dylib) was built for newer 
macOS version (10.15) than being linked (10.9)
ld: warning: dylib (/usr/local/lib/libntl.dylib) was built for newer 
macOS version (10.15) than being linked (10.9)

now I believe that this is caused by src/bin/sage-env which has the 
following code:

if [ "$UNAME" = "Darwin" ]; then
  export MACOSX_VERSION=`uname -r | awk -F. '{print $1}'`
  case "$SAGE_MACOSX_DEPLOYMENT_TARGET" in
  legacy)
# legacy behavior of the Sage distribution.
# set MACOSX_DEPLOYMENT_TARGET -- if set incorrectly, this can
# cause lots of random "Abort trap" issues on OSX. see trac
# #7095 for an example.
if [ $MACOSX_VERSION -ge 14 ]; then
# various packages have still have issues with
# two digit OS X versions
MACOSX_DEPLOYMENT_TARGET=10.9
else
MACOSX_DEPLOYMENT_TARGET=10.$[$MACOSX_VERSION-4]
fi
export MACOSX_DEPLOYMENT_TARGET
;;
  "")
# Do nothing
;;
  *)
# A fixed version set at configure time.
export MACOSX_DEPLOYMENT_TARGET=$SAGE_MACOSX_DEPLOYMENT_TARGET
;;
  esac

and I'm trying to understand where all of this is coming from.  The trac 
ticket this references is 11 years old and so I'm not sure it's an issue 
any more.

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[sage-devel] Re: make ptestlong on Big Sur

[Zachary Scherr]

For the record, I was able to get make ptestlong it to finish by doing:

ulimit -n 4096

On Friday, January 8, 2021 at 3:30:19 PM UTC-5 Zachary Scherr wrote:

> Interesting.  I've noticed the segfaults in the past, but never the "too 
> many open files" error.  I'll try to play around with my ulimit and see if 
> I can get the testing to finish.
>
> On Friday, January 8, 2021 at 1:21:20 PM UTC-5 Matthias Koeppe wrote:
>
>> I think this has started to show up, at least sporadically, with the 
>> multiprocessing changes made in/for python 3.8, see 
>> https://trac.sagemath.org/ticket/27754
>>
>> Something definitely needs fixing.
>>
>> On Friday, January 8, 2021 at 9:55:06 AM UTC-8 zsc...@gmail.com wrote:
>>
>>> Has anyone tried to run "make -j8 ptestlong" on Big Sur? Every time I 
>>> run it, doctesting breaks with the following traceback:
>>>
>>> Traceback (most recent call last):
>>>   File "/Users/zscherr/sage/develop/src/bin/sage-runtests", line 182, in 
>>> 
>>> err = DC.run()
>>>   File 
>>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/control.py",
>>>  
>>> line 1236, in run
>>> self.run_doctests()
>>>   File 
>>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/control.py",
>>>  
>>> line 937, in run_doctests
>>> self.dispatcher.dispatch()
>>>   File 
>>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
>>>  
>>> line 2040, in dispatch
>>> self.parallel_dispatch()
>>>   File 
>>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
>>>  
>>> line 1935, in parallel_dispatch
>>> w.start()  # This might take some time
>>>   File 
>>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
>>>  
>>> line 2207, in start
>>> super(DocTestWorker, self).start()
>>>   File 
>>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py",
>>>  
>>> line 121, in start
>>> self._popen = self._Popen(self)
>>>   File 
>>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py",
>>>  
>>> line 224, in _Popen
>>> return _default_context.get_context().Process._Popen(process_obj)
>>>   File 
>>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py",
>>>  
>>> line 277, in _Popen
>>> return Popen(process_obj)
>>>   File 
>>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py",
>>>  
>>> line 19, in __init__
>>> self._launch(process_obj)
>>>   File 
>>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py",
>>>  
>>> line 65, in _launch
>>> child_r, parent_w = os.pipe()
>>> OSError: [Errno 24] Too many open files
>>> make: *** [ptestlong] Error 1
>>>
>>> Since I was trying to test in parallel I don't know exactly what's going 
>>> on, but the last test that was attempted before this error was
>>>
>>> sage -t --long --warn-long 53.1 --random-seed=0 src/sage/doctest/test.py
>>>
>>> by itself this test seems to pass but causes a lot of random segfaults, 
>>> although this is with homebrew's python 3.9.1.
>>>
>>

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[sage-devel] Re: make ptestlong on Big Sur

[Zachary Scherr]

Interesting.  I've noticed the segfaults in the past, but never the "too 
many open files" error.  I'll try to play around with my ulimit and see if 
I can get the testing to finish.

On Friday, January 8, 2021 at 1:21:20 PM UTC-5 Matthias Koeppe wrote:

> I think this has started to show up, at least sporadically, with the 
> multiprocessing changes made in/for python 3.8, see 
> https://trac.sagemath.org/ticket/27754
>
> Something definitely needs fixing.
>
> On Friday, January 8, 2021 at 9:55:06 AM UTC-8 zsc...@gmail.com wrote:
>
>> Has anyone tried to run "make -j8 ptestlong" on Big Sur? Every time I run 
>> it, doctesting breaks with the following traceback:
>>
>> Traceback (most recent call last):
>>   File "/Users/zscherr/sage/develop/src/bin/sage-runtests", line 182, in 
>> 
>> err = DC.run()
>>   File 
>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/control.py",
>>  
>> line 1236, in run
>> self.run_doctests()
>>   File 
>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/control.py",
>>  
>> line 937, in run_doctests
>> self.dispatcher.dispatch()
>>   File 
>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
>>  
>> line 2040, in dispatch
>> self.parallel_dispatch()
>>   File 
>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
>>  
>> line 1935, in parallel_dispatch
>> w.start()  # This might take some time
>>   File 
>> "/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
>>  
>> line 2207, in start
>> super(DocTestWorker, self).start()
>>   File 
>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py",
>>  
>> line 121, in start
>> self._popen = self._Popen(self)
>>   File 
>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py",
>>  
>> line 224, in _Popen
>> return _default_context.get_context().Process._Popen(process_obj)
>>   File 
>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py",
>>  
>> line 277, in _Popen
>> return Popen(process_obj)
>>   File 
>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py",
>>  
>> line 19, in __init__
>> self._launch(process_obj)
>>   File 
>> "/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py",
>>  
>> line 65, in _launch
>> child_r, parent_w = os.pipe()
>> OSError: [Errno 24] Too many open files
>> make: *** [ptestlong] Error 1
>>
>> Since I was trying to test in parallel I don't know exactly what's going 
>> on, but the last test that was attempted before this error was
>>
>> sage -t --long --warn-long 53.1 --random-seed=0 src/sage/doctest/test.py
>>
>> by itself this test seems to pass but causes a lot of random segfaults, 
>> although this is with homebrew's python 3.9.1.
>>
>

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[sage-devel] make ptestlong on Big Sur

[Zachary Scherr]

Has anyone tried to run "make -j8 ptestlong" on Big Sur? Every time I run 
it, doctesting breaks with the following traceback:

Traceback (most recent call last):
  File "/Users/zscherr/sage/develop/src/bin/sage-runtests", line 182, in 

err = DC.run()
  File 
"/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/control.py",
 
line 1236, in run
self.run_doctests()
  File 
"/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/control.py",
 
line 937, in run_doctests
self.dispatcher.dispatch()
  File 
"/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
 
line 2040, in dispatch
self.parallel_dispatch()
  File 
"/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
 
line 1935, in parallel_dispatch
w.start()  # This might take some time
  File 
"/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/sage/doctest/forker.py",
 
line 2207, in start
super(DocTestWorker, self).start()
  File 
"/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/process.py",
 
line 121, in start
self._popen = self._Popen(self)
  File 
"/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py",
 
line 224, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
  File 
"/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py",
 
line 277, in _Popen
return Popen(process_obj)
  File 
"/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py",
 
line 19, in __init__
self._launch(process_obj)
  File 
"/usr/local/Cellar/python@3.9/3.9.1_4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/popen_fork.py",
 
line 65, in _launch
child_r, parent_w = os.pipe()
OSError: [Errno 24] Too many open files
make: *** [ptestlong] Error 1

Since I was trying to test in parallel I don't know exactly what's going 
on, but the last test that was attempted before this error was

sage -t --long --warn-long 53.1 --random-seed=0 src/sage/doctest/test.py

by itself this test seems to pass but causes a lot of random segfaults, 
although this is with homebrew's python 3.9.1.

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[sage-devel] Re: Build issue for wheel for scipy OS X Catalina

[Zachary Scherr]

Maybe somebody with more experience can answer, but the problem is likely 
caused by the fact that you used a prebuilt binary of sage and then tried 
to remake it on your own computer.  What tends to happen in this situation 
is that the prebuilt binary was built with a specific version of Xcode but 
then in the meantime Xcode is updated and when you try to remake sage it 
breaks because it's retained paths to libraries that have been changed by 
Xcode updates.

There are a few different options for installing Sage on Mac and getting it 
to work.

1.  Install it through homebrew cask and then apply the fix for ssl 
at https://github.com/3-manifolds/fix_mac_sage.  I have not personally 
tried this but I've seen others in this forum have success.

2.  Install it through anaconda.  This is currently my favorite approach 
since it is simple, fast, and everything just seems to work.  Directions 
are at https://doc.sagemath.org/html/en/installation/conda.html

3.  Install from source.  You can get directions 
from https://doc.sagemath.org/html/en/installation/source.html.  The basic 
workflow after you've extracted the archive would be to run:

>>> source .homebrew-build-env
>>> ./configure
>>> make -jNUM

   where NUM is the number of parallel processes you want to use in your 
build process.

On Thursday, January 7, 2021 at 2:43:47 PM UTC-5 jackwi...@gmail.com wrote:

> Hello all,
>
> I installed sage via homebrew on OS X 10.15.7 (Macbook Pro laptop) with 
> python3 version 3.8.5. (I'm not sure if I got python3 through homebrew, as 
> I also seem to have more copies of python lying about than I thought.) My 
> first issue was that a Jupyter page could not load due to being unable to 
> import the _ssl module, and the log suggested that I run "sage -f python." 
> Upon doing so, this eventually failed while compiling the wheel for scipy:
>
> [scipy-1.5.2] 
> 
> [scipy-1.5.2] Error building a wheel for scipy-1.5.2
> [scipy-1.5.2] 
> 
> [scipy-1.5.2]
> [scipy-1.5.2] real 2m19.074s
> [scipy-1.5.2] user 3m40.041s
> [scipy-1.5.2] sys 0m34.633s
> [scipy-1.5.2] 
> 
> [scipy-1.5.2] Error installing package scipy-1.5.2
> [scipy-1.5.2] 
> 
> [scipy-1.5.2] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
> [scipy-1.5.2] explaining the problem and including the log file
>
> I attempt to open the subshell
>
> cd 
> '/Applications/SageMath-9.2.app/Contents/Resources/sage/local/var/tmp/sage/build/scipy-1.5.2'
>  
> && '/Applications/SageMath-9.2.app/Contents/Resources/sage/sage' --buildsh
>
> and run "MACOSX_DEPLOYMENT_TARGET=11.0 make scipy", as I saw mentioned in 
> a recent thread titled "MACOSX_DEPLOYMENT_TARGET problems", but I think I 
> was mixing and matching wrong suggestions as this just told me there was no 
> rule to make scipy.
>
> I have attached the logfile from the failed "sage -f python" build here:
>
>
> /Applications/SageMath-9.2.app/Contents/Resources/sage/logs/pkgs/scipy-1.5.2.log
>
>
> Best,
>
>
> Jack
>

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[sage-devel] Re: MACOSX_DEPLOYMENT_TARGET problems

[Zachary Scherr]

I posted over on Trac, but I'm new to sage development so I'll repost here. 
 The cffi issue has been fixed in 1.14.4 so it's probably best to update 
that package.  I created a https://trac.sagemath.org/ticket/31128 to do 
this.

As for scipy, it's possible to get scipy to build in the terminal by doing

MACOSX_DEPLOYMENT_TARGET=11.0 make scipy

or

MACOSX_DEPLOYMENT_TARGET=11.1 make scipy.

This is exactly what homebrew's scipy formula does.  It appears that the 
issue is that gfortran doesn't like whole number versions.  There's a 
discussion about this on Iain Sandoe's ARM gcc fork at 
https://github.com/iains/gcc-darwin-arm64/issues/31#issuecomment-750343944

A sensible idea might be to set MACOSX_DEPLOYMENT_TARGET in the makefile 
for scipy, and then possibly unset it if it causes issues with other 
packages.

On Monday, December 14, 2020 at 5:40:09 PM UTC-5 John H Palmieri wrote:

> I can also produce a simple patch for the numpy issue. But scipy is also 
> failing, and I don't know how to fix that. I get
>
>   /usr/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup 
> -bundle -bundle -undefined dynamic_lookup 
> -L/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib
>  
> -Wl,-rpath,/Users/palmieri/Desktop/Sage/sage_builds/TESTING/TEMP/sage-9.3.beta3/local/lib
>  
> build/temp.macosx-11-x86_64-3.9/scipy/integrate/_quadpackmodule.o 
> -L/usr/local/Cellar/openblas/0.3.12_1/lib 
> -L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/gcc/x86_64-apple-darwin20/10.2.0 
> -L/usr/local/lib -L/usr/local/lib -L/usr/local/lib 
> -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/sqlite/lib 
> -Lbuild/temp.macosx-11-x86_64-3.9 -lquadpack -lmach -lopenblas -lopenblas 
> -lgfortran -o build/lib.macosx-11-x86_64-3.9/scipy/integrate/_
> quadpack.cpython-39-darwin.so
>   gfortran: warning: couldn't understand version 11
>   ld: library not found for -lgcc_s.10.4
>   collect2: error: ld returned 1 exit status
>
> Any suggestions would be appreciated.
>
> On Monday, December 14, 2020 at 1:37:22 PM UTC-8 John H Palmieri wrote:
>
>> I am having problems building Sage with a recently updated homebrew 
>> Python 3.9 on OS X Big Sur, apparently because it sets 
>> MACOSX_DEPLOYMENT_TARGET to 11. (Insert Spinal Tap joke here.) If you run 
>> `brew update` on Big Sur, I'm guessing that you will run into this.
>>
>> - There is a problem because of wheel: see https://github.com/pypa/
>> wheel/issues/385. (Update at #31050.) This leads to failures when 
>> building gmpy2 and cython.
>>
>> - There is a problem with cffi because its setup.py has
>>
>> get_config_var("MACOSX_DEPLOYMENT_TARGET").split('.')
>>
>> This fails because `get_config_var` returns an `int` in this case rather 
>> than a string.
>>
>> (No trac ticket yet. The most recent version of cffi doesn't fix this, as 
>> far as I can tell, but it's easy to write a patch.)
>>
>> - There is a similar problem with numpy:
>>
>> os.environ['MACOSX_DEPLOYMENT_TARGET'] = target
>> ...
>>TypeError: str expected, not int
>>
>> I haven't tried to fix that one yet, so I don't know if there are more 
>> problems.
>>
>> -- 
>> John
>>
>>

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[sage-devel] Re: pillow-7.2.0 build issue with homebrew libzip

[Zachary Scherr]

I have not.  I just sourced .homebrew-build-env and then built in the 
normal way.  I haven't had this problem in the past, but I'm not sure when 
homebrew installed libzip on my laptop (I see it is a dependency of php).

I can see in the failing gcc command that -I/usr/local/include comes 
before 
-I/Users/zscherr/temp/sage/local/var/tmp/sage/build/pillow-7.2.0/src/src/libImaging
 
so that could be why it finds zip.h before Zip.h

I took a look at the most recent version of Pillow and it seems like they 
solved the issue by renaming Zip.h to ZipCodecs.h.

On Tuesday, December 15, 2020 at 8:30:45 PM UTC-5 Matthias Koeppe wrote:

> We had the same problem previously - 
> https://trac.sagemath.org/ticket/29562
> Have you set CPPFLAGS by any chance?
>
> On Tuesday, December 15, 2020 at 12:26:26 PM UTC-8 zsc...@gmail.com wrote:
>
>> I just tried building 9.3.beta4 and my build breaks at pillow-7.2.0 on 
>> Catalina 10.15.7.
>>
>> The actual error is:
>>
>> [pillow-7.2.0]   gcc -Wno-unused-result -Wsign-compare -Wunreachable-code 
>> -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include 
>> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk 
>> -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include 
>> -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
>>  
>> -O2 -g -g -DHAVE_OPENJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -DHAVE_XCB 
>> -DPILLOW_VERSION="7.2.0" 
>> -I/usr/local/Cellar/openjpeg/2.3.1/include/openjpeg-2.3 
>> -I/Users/zscherr/sage/develop/local/var/tmp/sage/build/pillow-7.2.0/src/src/libImaging
>>  
>> -I/usr/local/Cellar/jpeg/9d/include 
>> -I/usr/local/Cellar/libtiff/4.1.0_1/include 
>> -I/Users/zscherr/sage/develop/local/var/tmp/sage/build/pillow-7.2.0/src 
>> -I/usr/local/Cellar/freetype/2.10.4/include/freetype2 
>> -I/usr/local/Cellar/little-cms2/2.11/include 
>> -I/Users/zscherr/sage/develop/local/include 
>> -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include 
>> -I/usr/local/include -I/usr/local/Cellar/freetype/2.10.4/include 
>> -I/usr/local/include -I/usr/local/opt/openssl@1.1/include 
>> -I/usr/local/opt/sqlite/include -I/Users/zscherr/sage/develop/local/include 
>> -I/usr/local/Cellar/python@3.9/3.9.1/Frameworks/Python.framework/Versions/3.9/include/python3.9
>>  
>> -c src/decode.c -o build/temp.macosx-10.15-x86_64-3.9/src/decode.o
>>   [pillow-7.2.0]   src/decode.c:810:10: warning: non-portable path to 
>> file '"zip.h"'; specified path differs in case from file name on disk 
>> [-Wnonportable-include-path]
>>   [pillow-7.2.0]   #include "Zip.h"
>>   [pillow-7.2.0]^~~
>>   [pillow-7.2.0]"zip.h"
>>   [pillow-7.2.0]   src/decode.c:824:43: error: use of undeclared 
>> identifier 'ZIPSTATE'
>>   [pillow-7.2.0]   decoder = PyImaging_DecoderNew(sizeof(ZIPSTATE));
>>   [pillow-7.2.0] ^
>>   [pillow-7.2.0]   src/decode.c:836:16: error: expected expression
>>   [pillow-7.2.0]   ((ZIPSTATE*)decoder->state.context)->interlaced = 
>> interlaced;
>>   [pillow-7.2.0]  ^
>>   [pillow-7.2.0]   src/decode.c:836:7: error: use of undeclared 
>> identifier 'ZIPSTATE'
>>   [pillow-7.2.0]   ((ZIPSTATE*)decoder->state.context)->interlaced = 
>> interlaced;
>>   [pillow-7.2.0] ^
>>   [pillow-7.2.0]   1 warning and 3 errors generated.
>>   [pillow-7.2.0]   gcc -bundle -undefined dynamic_lookup -L/usr/local/lib 
>> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk 
>> -L/Users/zscherr/sage/develop/local/lib 
>> -Wl,-rpath,/Users/zscherr/sage/develop/local/lib -O2 -g -g 
>> build/temp.macosx-10.15-x86_64-3.9/src/_imagingmath.o 
>> -L/usr/local/Cellar/jpeg/9d/lib -L/usr/local/Cellar/openjpeg/2.3.1/lib 
>> -L/usr/local/Cellar/libtiff/4.1.0_1/lib 
>> -L/Users/zscherr/sage/develop/local/var/tmp/sage/build/pillow-7.2.0/src 
>> -L/usr/local/Cellar/freetype/2.10.4/lib 
>> -L/usr/local/Cellar/little-cms2/2.11/lib 
>> -L/Users/zscherr/sage/develop/local/lib -L/usr/local/lib -L/usr/lib 
>> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib 
>> -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.15-x86_64-3.9/PIL/_
>> imagingmath.cpython-39-darwin.so
>>   [pillow-7.2.0]   error: command '/usr/bin/gcc' failed with exit code 1
>>
>> 
>>
>> From what I can tell, I have libzip installed with homebrew, which puts a 
>> zip.h symlink in my /usr/local/include directory.  It would appear that the 
>> pillow makefile is picking up this zip.h as opposed to the Zip.h that comes 
>> with pillow.
>>
>> I can fix this problem via
>>
>> brew unlink libzip
>> make pillow
>> brew link libzip
>>
>> so I'm guessing it probably requires an easy modification to the pillow 
>> makefile.
>>
>

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[sage-devel] Re: fpylll not building - Cataline 10.15.7

[Zachary Scherr]

Hi Matthias,

   Thank you.  I had forgotten I had fplll installed via homebrew, removing 
it fixed my problem.

On Tuesday, December 15, 2020 at 8:32:52 PM UTC-5 Matthias Koeppe wrote:

> Is this with fplll from homebrew? 
> Only specific versions of fplll and fpylll work together - in 
> https://trac.sagemath.org/ticket/31025 we upgrade and tighten what 
> versions we accept.
>
> On Tuesday, December 15, 2020 at 1:47:37 PM UTC-8 zsc...@gmail.com wrote:
>
>> Sorry for the spam today, but after fixing my pillow issue I encountered 
>> a problem with fpylll on 9.3.beta4.  The key lines seem to be:
>>
>>   build/src/fpylll/fplll/integer_matrix.cpp:706:10: fatal error: 
>> 'fplll/sieve/sieve_gauss.h' file not found
>>   #include "fplll/sieve/sieve_gauss.h"
>>^~~
>>   1 error generated.
>>
>> I've attached the config file, but I wonder if something is wrong with 
>> the upstream tarball.
>>
>

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[sage-devel] fpylll not building - Cataline 10.15.7

[Zachary Scherr]

Sorry for the spam today, but after fixing my pillow issue I encountered a 
problem with fpylll on 9.3.beta4.  The key lines seem to be:

  build/src/fpylll/fplll/integer_matrix.cpp:706:10: fatal error: 
'fplll/sieve/sieve_gauss.h' file not found
  #include "fplll/sieve/sieve_gauss.h"
   ^~~
  1 error generated.

I've attached the config file, but I wonder if something is wrong with the 
upstream tarball.

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Found local metadata for fpylll-0.5.2dev
Using cached file /Users/zscherr/sage/develop/upstream/fpylll-0.5.2dev.tar.gz
fpylll-0.5.2dev

Setting up build directory for fpylll-0.5.2dev
Finished extraction
No patch files found in ../patches

Host system:
Darwin Zacharys-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Tue Nov 
10 00:10:30 PST 2020; root:xnu-6153.141.10~1/RELEASE_X86_64 x86_64

C compiler: gcc
C compiler version:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.28)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Package 'fpylll' is currently not installed
No legacy uninstaller found for 'fpylll'; nothing to do
Installing fpylll-0.5.2dev
Ignoring indexes: https://pypi.org/simple
Created temporary directory: 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-ephem-wheel-cache-lv3ob_uk
Created temporary directory: 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-tracker-g4dy8tu7
Initialized build tracking at 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-tracker-g4dy8tu7
Created build tracker: 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-tracker-g4dy8tu7
Entered build tracker: 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-tracker-g4dy8tu7
Created temporary directory: 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-wheel-wcmyluq7
Processing 
/Users/zscherr/sage/develop/local/var/tmp/sage/build/fpylll-0.5.2dev/src
  Created temporary directory: 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-build-acmh4trl
  Added 
file:///Users/zscherr/sage/develop/local/var/tmp/sage/build/fpylll-0.5.2dev/src 
to build tracker 
'/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-tracker-g4dy8tu7'
Running setup.py 
(path:/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-build-acmh4trl/setup.py)
 egg_info for package from 
file:///Users/zscherr/sage/develop/local/var/tmp/sage/build/fpylll-0.5.2dev/src
Created temporary directory: 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q
Running command python setup.py egg_info

/Users/zscherr/sage/develop/local/lib/python3.9/site-packages/setuptools/dist.py:458:
 UserWarning: Normalizing '0.5.2dev' to '0.5.2.dev0'
  warnings.warn(tmpl.format(**locals()))
running egg_info
creating 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q/fpylll.egg-info
writing 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q/fpylll.egg-info/PKG-INFO
writing dependency_links to 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q/fpylll.egg-info/dependency_links.txt
writing top-level names to 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q/fpylll.egg-info/top_level.txt
writing manifest file 
'/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q/fpylll.egg-info/SOURCES.txt'
reading manifest file 
'/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q/fpylll.egg-info/SOURCES.txt'
writing manifest file 
'/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-pip-egg-info-_0x4520q/fpylll.egg-info/SOURCES.txt'
  Source in 
/private/var/folders/5f/z870t4kd5dlctkcrs984nh8rgn/T/pip-req-build-acmh4trl 
has version 0.5.2.dev0, which satisfies requirement fpylll==0.5.2.dev0 from 
file:///Users/zscherr/sage/develop/local/var/tmp/sage/build/fpylll-0.5.2dev/src
  Removed fpylll==0.5.2.dev0 from 
file:///Users/zscherr/sage/develop/local/var/tmp/sage/build/fpylll-0.5.2dev/src 
from build tracker 

Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7

[Zachary Scherr]

You can safely ignore that message.  I think there is some ongoing work 
being done on changing how sage handles recommended packages and that 
message is a byproduct.  If it's really bothering you then you can just 
type:

make _recommended

and I think that message should disappear.

On Tuesday, December 15, 2020 at 3:24:12 PM UTC-5 vanhove...@gmail.com 
wrote:

> hi
>
> I have cleanup my /usr/local  - reinstalled a fresh brew  and Xcode.
> I have run ./configure in sage-9.3-beta4 that complained about missing 
> homebrew package. I have installed them.
> % brew list
> aom fribidi harfbuzz libheif little-cms2 pandoc srt
> arb gcc icu4c libidn2 lzo pcre suite-sparse
> bdw-gc gd igraph liblqr metis pcre2 tbb
> boost gdbm ilmbase libmpc mpfi pixman tesseract
> c-ares gettext imagemagick libogg mpfr pkg-config texinfo
> cairo ghostscript isl libomp nauty ppl theora
> cmake giflib jemalloc libpng nettle python@3.9 tox
> coreutils glib jpeg libsamplerate nghttp2 r unbound
> dav1d glpk lame libsndfile ninja rav1e webp
> docbook gmp leptonica libsoxr ntl readline x264
> docbook-xsl gnu-getopt libass libtasn1 openblas rtmpdump x265
> ffmpeg gnutls libatomic_ops libtiff opencore-amr rubberband xmlto
> flac gobject-introspection libbluray libtool openexr sdl2 xvid
> flint gpatch libde265 libunistring openjpeg shared-mime-info xz
> fontconfig graphite2 libev libvidstab openssl@1.1 snappy zeromq
> freetype gsl libevent libvorbis opus speex
> frei0r guile libffi libvpx p11-kit sqlite
>
> my homebrew setup is clean 
>
> % brew doctor
> Your system is ready to brew.
>
> then   boostrapping, sourcing brew environnement and rerun configure in 
> sage, I still get the message
>
>$ brew install pandoc ffmpeg imagemagick texinfo
>
>
> Pierre
>
> Le mardi 15 décembre 2020 à 19:57:40 UTC+1, zsc...@gmail.com a écrit :
>
>> Have you tried running "brew doctor"? Homebrew should complain loudly 
>> about all of the header files in /usr/local/include which could cause 
>> conflicts.  For example, if I touch stdio.h in my /usr/local/include and 
>> then I run brew doctor I get:
>>
>> "Warning: Unbrewed header files were found in /usr/local/include.
>> If you didn't put them there on purpose they could cause problems when
>> building Homebrew formulae, and may need to be deleted.
>>
>> Unexpected header files:
>>   /usr/local/include/stdio.h"
>>
>> I would start with running brew doctor and trying to fix the 
>> recommendations there.
>>
>> On Tuesday, December 15, 2020 at 8:43:28 AM UTC-5 dim...@gmail.com wrote:
>>
>>> On Tue, Dec 15, 2020 at 1:23 PM Pierre Vanhove  
>>> wrote: 
>>> > 
>>> > hi 
>>> > 
>>> > 
>>> > What did one do yesterday just after 17:00 on the machine? 
>>> > Updated Homebrew? Installed macOS command line tools? 
>>> > 
>>> > 
>>> > yes I updated homebrew, but with a bad internet connection and the 
>>> connection broke. I had to redo it. 
>>> > 
>>> > But curiously, I have deleted the sage-9.2 folder downloaded a 
>>> sage-9.3-beta4 and then worked from the new folder. 
>>> > 
>>> > I will see if using the backup from my time machine solves the problem 
>>> by going back in time. 
>>>
>>> I'd suggest to install the full XCode. The fact that homebrew 
>>> apparently created that link indicates 
>>> that not all is well; I'd also erase the whole /usr/local and 
>>> reinstall Homebrew from scratch, 
>>> after XCode is installed. 
>>>
>>> macOS, Homebrew, XCode are moving targets, it's hard to keep up with 
>>> them. 
>>>
>>> > 
>>> > Now that they have put sirocco on cocacl, I will work with that. And I 
>>> will leave most of the sage coding to Andrey Novoseltsev then since locally 
>>> I cannot work... 
>>> > 
>>> > best, Pierre 
>>> > 
>>> >  
>>> > Pierre Vanhove (vanhove...@gmail.com) | web: 
>>> http://sites.google.com/site/vanhovepierre/ 
>>> > 
>>> > 
>>> > 
>>> > 
>>> > 
>>> > 
>>> > -- 
>>> > 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/95B792F4-B444-4DBB-8E4B-2846A020C683%40gmail.com.
>>>  
>>>
>>>
>>

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[sage-devel] pillow-7.2.0 build issue with homebrew libzip

[Zachary Scherr]

I just tried building 9.3.beta4 and my build breaks at pillow-7.2.0 on 
Catalina 10.15.7.

The actual error is:

[pillow-7.2.0]   gcc -Wno-unused-result -Wsign-compare -Wunreachable-code 
-fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include 
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk 
-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include 
-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
 
-O2 -g -g -DHAVE_OPENJPEG -DHAVE_LIBZ -DHAVE_LIBTIFF -DHAVE_XCB 
-DPILLOW_VERSION="7.2.0" 
-I/usr/local/Cellar/openjpeg/2.3.1/include/openjpeg-2.3 
-I/Users/zscherr/sage/develop/local/var/tmp/sage/build/pillow-7.2.0/src/src/libImaging
 
-I/usr/local/Cellar/jpeg/9d/include 
-I/usr/local/Cellar/libtiff/4.1.0_1/include 
-I/Users/zscherr/sage/develop/local/var/tmp/sage/build/pillow-7.2.0/src 
-I/usr/local/Cellar/freetype/2.10.4/include/freetype2 
-I/usr/local/Cellar/little-cms2/2.11/include 
-I/Users/zscherr/sage/develop/local/include 
-I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include 
-I/usr/local/include -I/usr/local/Cellar/freetype/2.10.4/include 
-I/usr/local/include -I/usr/local/opt/openssl@1.1/include 
-I/usr/local/opt/sqlite/include -I/Users/zscherr/sage/develop/local/include 
-I/usr/local/Cellar/python@3.9/3.9.1/Frameworks/Python.framework/Versions/3.9/include/python3.9
 
-c src/decode.c -o build/temp.macosx-10.15-x86_64-3.9/src/decode.o
  [pillow-7.2.0]   src/decode.c:810:10: warning: non-portable path to file 
'"zip.h"'; specified path differs in case from file name on disk 
[-Wnonportable-include-path]
  [pillow-7.2.0]   #include "Zip.h"
  [pillow-7.2.0]^~~
  [pillow-7.2.0]"zip.h"
  [pillow-7.2.0]   src/decode.c:824:43: error: use of undeclared identifier 
'ZIPSTATE'
  [pillow-7.2.0]   decoder = PyImaging_DecoderNew(sizeof(ZIPSTATE));
  [pillow-7.2.0] ^
  [pillow-7.2.0]   src/decode.c:836:16: error: expected expression
  [pillow-7.2.0]   ((ZIPSTATE*)decoder->state.context)->interlaced = 
interlaced;
  [pillow-7.2.0]  ^
  [pillow-7.2.0]   src/decode.c:836:7: error: use of undeclared identifier 
'ZIPSTATE'
  [pillow-7.2.0]   ((ZIPSTATE*)decoder->state.context)->interlaced = 
interlaced;
  [pillow-7.2.0] ^
  [pillow-7.2.0]   1 warning and 3 errors generated.
  [pillow-7.2.0]   gcc -bundle -undefined dynamic_lookup -L/usr/local/lib 
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk 
-L/Users/zscherr/sage/develop/local/lib 
-Wl,-rpath,/Users/zscherr/sage/develop/local/lib -O2 -g -g 
build/temp.macosx-10.15-x86_64-3.9/src/_imagingmath.o 
-L/usr/local/Cellar/jpeg/9d/lib -L/usr/local/Cellar/openjpeg/2.3.1/lib 
-L/usr/local/Cellar/libtiff/4.1.0_1/lib 
-L/Users/zscherr/sage/develop/local/var/tmp/sage/build/pillow-7.2.0/src 
-L/usr/local/Cellar/freetype/2.10.4/lib 
-L/usr/local/Cellar/little-cms2/2.11/lib 
-L/Users/zscherr/sage/develop/local/lib -L/usr/local/lib -L/usr/lib 
-L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib 
-L/usr/local/opt/sqlite/lib -o 
build/lib.macosx-10.15-x86_64-3.9/PIL/_imagingmath.cpython-39-darwin.so
  [pillow-7.2.0]   error: command '/usr/bin/gcc' failed with exit code 1



>From what I can tell, I have libzip installed with homebrew, which puts a 
zip.h symlink in my /usr/local/include directory.  It would appear that the 
pillow makefile is picking up this zip.h as opposed to the Zip.h that comes 
with pillow.

I can fix this problem via

brew unlink libzip
make pillow
brew link libzip

so I'm guessing it probably requires an easy modification to the pillow 
makefile.

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Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7

[Zachary Scherr]

Have you tried running "brew doctor"? Homebrew should complain loudly about 
all of the header files in /usr/local/include which could cause conflicts. 
 For example, if I touch stdio.h in my /usr/local/include and then I run 
brew doctor I get:

"Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
  /usr/local/include/stdio.h"

I would start with running brew doctor and trying to fix the 
recommendations there.

On Tuesday, December 15, 2020 at 8:43:28 AM UTC-5 dim...@gmail.com wrote:

> On Tue, Dec 15, 2020 at 1:23 PM Pierre Vanhove  
> wrote:
> >
> > hi
> >
> >
> > What did one do yesterday just after 17:00 on the machine?
> > Updated Homebrew? Installed macOS command line tools?
> >
> >
> > yes I updated homebrew, but with a bad internet connection and the 
> connection broke. I had to redo it.
> >
> > But curiously, I have deleted the sage-9.2 folder downloaded a 
> sage-9.3-beta4 and then worked from the new folder.
> >
> > I will see if using the backup from my time machine solves the problem 
> by going back in time.
>
> I'd suggest to install the full XCode. The fact that homebrew
> apparently created that link indicates
> that not all is well; I'd also erase the whole /usr/local and
> reinstall Homebrew from scratch,
> after XCode is installed.
>
> macOS, Homebrew, XCode are moving targets, it's hard to keep up with them.
>
> >
> > Now that they have put sirocco on cocacl, I will work with that. And I 
> will leave most of the sage coding to Andrey Novoseltsev then since locally 
> I cannot work...
> >
> > best, Pierre
> >
> > 
> > Pierre Vanhove (vanhove...@gmail.com) | web: 
> http://sites.google.com/site/vanhovepierre/
> >
> >
> >
> >
> >
> >
> > --
> > 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/95B792F4-B444-4DBB-8E4B-2846A020C683%40gmail.com
> .
>

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[sage-devel] Re: parallel compilation does not work anymore

[Zachary Scherr]

Just wanted to add that make -j8 doc is also not building in parallel.

On Wednesday, December 2, 2020 at 10:35:05 AM UTC-5 Eric Gourgoulhon wrote:

> Le mercredi 2 décembre 2020 à 14:20:56 UTC+1, vdelecroix a écrit :
>
>> Dear all, 
>>
>> For the 9.3.beta2 release the command 
>>
>> $ MAKE="make -j3" make build 
>>
>> does not compile the Cython code of the sagelib in parallel. 
>> This slows down a lot the build of the library. I am sure 
>> when it stopped working. 
>>
>
> I confirm: on my Ubuntu 20.04 machine,  
> MAKE="make -j8" make 
> took ages to build 9.3.beta2 (from 9.3.beta1), exactly because the Cython 
> part of sagelib.
> I have not noticed such an issue with 9.3.beta1.
>
> Eric.
>
>
>

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[sage-devel] Re: Apple M1 Chip

[Zachary Scherr]

You may want to take a look at with 
https://github.com/Homebrew/brew/issues/7857.  I think the biggest thing at 
the moment is that gfortran won't be available for the M1 for some time.

On Tuesday, November 24, 2020 at 10:47:42 AM UTC-5 kcrisman wrote:

> Hi sage-devel,
>
> The only references I could find to this so far are
> https://ask.sagemath.org/question/54220/apple-silicon-m1-chip/
> and 
> https://groups.google.com/g/sage-devel/c/5yY3VmkT4kE/m/P21QdaMUBgAJ
> where I asked more generally about ARM.
>
> I am likely to be assigned such a laptop in the near future, but it would 
> be nice not to be a total guinea pig (since I rely on having Sage for a 
> number of different purposes in my teaching).  Though I am willing to be a 
> partial guinea pig if I get the computer early enough in our semester break!
>
> Anyway, in the intervening weeks since those posts, has anyone happened to 
> hear more about this (either for Sage or for dependencies like 
> BLAS/Numpy/MPIR)?  This will be the default for a lot of people pretty soon.
>
> Thanks, 
> kcrisman
>

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Re: [sage-devel] Building Sage 9.2 on Mac fails due to cysignals

[Zachary Scherr]

Did you by any chance install fortran via:

brew cask install gfortran?

from your config.log file it finds gfortran version 8, but the most recent 
homebrew fortran is 10.2.

Maybe try uninstalling gfortran and then either brew install gcc or brew 
reinstall gcc to get a more up to date fortran.  For example on my Mac when 
I run gfortran --version I get:

GNU Fortran (Homebrew GCC 10.2.0) 10.2.0

On Thursday, October 29, 2020 at 12:34:30 PM UTC-4 modp...@gmail.com wrote:

> Okay rebuilding PARI without -mt=pthread option worked. 
> But now building the documentation fails. Please find the log file 
> attached.
> Anyway, I currently build it without documentation by running 'make build' 
> only.
> But was curious why documentation fails.
>
> On Wednesday, October 28, 2020 at 8:01:43 PM UTC+1 dim...@gmail.com wrote:
>
>>
>>
>> On Wed, 28 Oct 2020, 14:33 Zachary Scherr,  wrote:
>>
>>> Hopefully somebody with more experience can weigh in, but for the record 
>>> I have pari installed via homebrew and there the configure is only with 
>>> --with-gmp and --with-readline and that works with building sage.  It's 
>>> plausible that the -mt=pthread is what's causing the issues.
>>>
>>
>> Hombrew does not provide Pari packages. Unless you install them manually 
>> (these are just data files)
>> it will not be used by Sage.
>>
>> If you install Pari with  -mt=pthread
>> into /usr/local, with its packages, it will be accepted by Sage, causing 
>> this problem.
>>
>> Patches to fix this are welcome.
>> Ideally it can be a short C program to link against libpari, which would 
>> fail with the error message reported on this thread.
>>
>>
>>
>>
>>> On Wednesday, October 28, 2020 at 10:12:35 AM UTC-4 modp...@gmail.com 
>>> wrote:
>>>
>>>> Yes, I have manually installed Pari 2.11.4 after configuring it with:
>>>> Confgure --mt=pthread --tune
>>>>
>>>> On Wednesday, October 28, 2020 at 3:04:01 PM UTC+1 zsc...@gmail.com 
>>>> wrote:
>>>>
>>>>> Just wanted to make a couple of comments.  First off, brew installs 
>>>>> llvm as keg-only meaning that sage shouldn't even be able to find it 
>>>>> unless 
>>>>> you manually added something like:
>>>>>
>>>>> export PATH="/usr/local/opt/llvm/bin:$PATH"
>>>>> export LDFLAGS="-L/usr/local/opt/llvm/lib"
>>>>> export CPPFLAGS="-I/usr/local/opt/llvm/include"
>>>>>
>>>>> to your profile.  But even after I tried that myself, I failed to 
>>>>> reproduce your error on my own Mac machine.  This makes me think that you 
>>>>> might want to have a look at the version of Pari you installed on your 
>>>>> computer.  I noticed that ./configure finds a copy of Pari in /usr/local 
>>>>> on 
>>>>> your computer.  You can see that the specific error it references 
>>>>> mentions:
>>>>>
>>>>>  ld: illegal thread local variable reference to regular symbol 
>>>>> _PARI_SIGINT_block for architecture x86_64
>>>>>
>>>>> If removing llvm and make distclean doesn't solve your problem then 
>>>>> you may want to look into where you got your Pari.  It seems plausible 
>>>>> that 
>>>>> Pari might have been built in some funky way and that is what's causing 
>>>>> your issue. 
>>>>> On Wednesday, October 28, 2020 at 7:27:27 AM UTC-4 dim...@gmail.com 
>>>>> wrote:
>>>>>
>>>>>> try 
>>>>>> make distclean
>>>>>>
>>>>>> and the build 
>>>>>>
>>>>>> On Wed, 28 Oct 2020, 09:57 modp...@gmail.com,  
>>>>>> wrote:
>>>>>>
>>>>>>>
>>>>>>> I tried uninstalling LLVM and building it again, but it fails again 
>>>>>>> for cysignals. 
>>>>>>> But the problem now seems that it still sets -I and -L flags with 
>>>>>>> non-existent LLVM directories.
>>>>>>> On Tuesday, October 27, 2020 at 5:10:58 PM UTC+1 Matthias Koeppe 
>>>>>>> wrote:
>>>>>>>
>>>>>>>> From config.log:
>>>>>>>>
>>>>>>>> configure:5906: gcc -v >&5
>>>>>>>> Configured with: 
>>>>>>>> --prefix=/Applic

Re: [sage-devel] Building Sage 9.2 on Mac fails due to cysignals

[Zachary Scherr]

Hopefully somebody with more experience can weigh in, but for the record I 
have pari installed via homebrew and there the configure is only with 
--with-gmp and --with-readline and that works with building sage.  It's 
plausible that the -mt=pthread is what's causing the issues.

On Wednesday, October 28, 2020 at 10:12:35 AM UTC-4 modp...@gmail.com wrote:

> Yes, I have manually installed Pari 2.11.4 after configuring it with:
> Confgure --mt=pthread --tune
>
> On Wednesday, October 28, 2020 at 3:04:01 PM UTC+1 zsc...@gmail.com wrote:
>
>> Just wanted to make a couple of comments.  First off, brew installs llvm 
>> as keg-only meaning that sage shouldn't even be able to find it unless you 
>> manually added something like:
>>
>> export PATH="/usr/local/opt/llvm/bin:$PATH"
>> export LDFLAGS="-L/usr/local/opt/llvm/lib"
>> export CPPFLAGS="-I/usr/local/opt/llvm/include"
>>
>> to your profile.  But even after I tried that myself, I failed to 
>> reproduce your error on my own Mac machine.  This makes me think that you 
>> might want to have a look at the version of Pari you installed on your 
>> computer.  I noticed that ./configure finds a copy of Pari in /usr/local on 
>> your computer.  You can see that the specific error it references mentions:
>>
>>  ld: illegal thread local variable reference to regular symbol 
>> _PARI_SIGINT_block for architecture x86_64
>>
>> If removing llvm and make distclean doesn't solve your problem then you 
>> may want to look into where you got your Pari.  It seems plausible that 
>> Pari might have been built in some funky way and that is what's causing 
>> your issue. 
>> On Wednesday, October 28, 2020 at 7:27:27 AM UTC-4 dim...@gmail.com 
>> wrote:
>>
>>> try 
>>> make distclean
>>>
>>> and the build 
>>>
>>> On Wed, 28 Oct 2020, 09:57 modp...@gmail.com,  wrote:
>>>

 I tried uninstalling LLVM and building it again, but it fails again for 
 cysignals. 
 But the problem now seems that it still sets -I and -L flags with 
 non-existent LLVM directories.
 On Tuesday, October 27, 2020 at 5:10:58 PM UTC+1 Matthias Koeppe wrote:

> From config.log:
>
> configure:5906: gcc -v >&5
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
> Apple clang version 12.0.0 (clang-1200.0.32.21)
> Target: x86_64-apple-darwin19.6.0
> Thread model: posix
> InstalledDir: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
> configure:5917: $? = 0
> ...
>
> configure:6029: gcc -o conftest  -I/usr/local/opt/llvm/include 
> -L/usr/local/opt/llvm/lib conftest.c  >&5
>
>
> This looks like an unsupported configuration - injecting these -L and 
> -I flags via environment variables, but continuing to use Apple's gcc.
> If you are trying to compile with homebrew's llvm, you should probably 
> configure by setting CC and CXX as well. But this is also untested - I 
> have 
> created https://trac.sagemath.org/ticket/30835#ticket for testing 
> such a configuration.
>
>
> On Tuesday, October 27, 2020 at 3:46:10 AM UTC-7, Dima Pasechnik wrote:
>
>> I'd have tried removing llvm and trying again. Perhaps this is a 
>> conflict between Homebrew packages.
>>
>> On Tue, Oct 27, 2020 at 8:42 AM modp...@gmail.com  
>> wrote:
>>
> Please find config.log and cysignals-1.10.2.log attached. I already 
>>> run "source .homebrew-build-env" before configuring.
>>> And yes I also have llvm installed through Homebrew.
>>>
>>> On Monday, October 26, 2020 at 3:23:38 PM UTC+1 dim...@gmail.com 
>>> wrote:
>>>
 also note that you apparently have something in 
 -L/usr/local/opt/llvm/lib (installed from Homebrew ?) which might 
 lead 
 to surprises. 
 Do you have some LDFLAGS set? 
 It would help if you also post logs/pkgs/cysignals-1.10.2.log 

 On Mon, Oct 26, 2020 at 2:15 PM Dima Pasechnik  
 wrote: 
 > 
 > also, if you have Homebrew, you should run 
 > 
 > source .homebrew-build-env 
 > 
 > before 
 > 
 > ./configure 
 > 
 > On Mon, Oct 26, 2020 at 1:50 PM Dima Pasechnik  
 wrote: 
 >> 
 >> please post the top-level config.log here 
 >> 
 >> On Mon, 26 Oct 2020, 13:45 modp...@gmail.com,  
 wrote: 
 >>> 
 >>> 
 >>> I'm building Sage 9.2 from source on macOS Catalina 10.15.7, 
 however, it fails 
 >>> when trying to install cysignals. More precisely, it throws the 
 following error: 
 >>> 
 >>> gcc -bundle -undefined dynamic_lookup -isysroot 
 

Re: [sage-devel] Building Sage 9.2 on Mac fails due to cysignals

[Zachary Scherr]

Just wanted to make a couple of comments.  First off, brew installs llvm as 
keg-only meaning that sage shouldn't even be able to find it unless you 
manually added something like:

export PATH="/usr/local/opt/llvm/bin:$PATH"
export LDFLAGS="-L/usr/local/opt/llvm/lib"
export CPPFLAGS="-I/usr/local/opt/llvm/include"

to your profile.  But even after I tried that myself, I failed to reproduce 
your error on my own Mac machine.  This makes me think that you might want 
to have a look at the version of Pari you installed on your computer.  I 
noticed that ./configure finds a copy of Pari in /usr/local on your 
computer.  You can see that the specific error it references mentions:

 ld: illegal thread local variable reference to regular symbol 
_PARI_SIGINT_block for architecture x86_64

If removing llvm and make distclean doesn't solve your problem then you may 
want to look into where you got your Pari.  It seems plausible that Pari 
might have been built in some funky way and that is what's causing your 
issue. 
On Wednesday, October 28, 2020 at 7:27:27 AM UTC-4 dim...@gmail.com wrote:

> try 
> make distclean
>
> and the build 
>
> On Wed, 28 Oct 2020, 09:57 modp...@gmail.com,  wrote:
>
>>
>> I tried uninstalling LLVM and building it again, but it fails again for 
>> cysignals. 
>> But the problem now seems that it still sets -I and -L flags with 
>> non-existent LLVM directories.
>> On Tuesday, October 27, 2020 at 5:10:58 PM UTC+1 Matthias Koeppe wrote:
>>
>>> From config.log:
>>>
>>> configure:5906: gcc -v >&5
>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
>>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
>>> Apple clang version 12.0.0 (clang-1200.0.32.21)
>>> Target: x86_64-apple-darwin19.6.0
>>> Thread model: posix
>>> InstalledDir: 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>> configure:5917: $? = 0
>>> ...
>>>
>>> configure:6029: gcc -o conftest  -I/usr/local/opt/llvm/include 
>>> -L/usr/local/opt/llvm/lib conftest.c  >&5
>>>
>>>
>>> This looks like an unsupported configuration - injecting these -L and -I 
>>> flags via environment variables, but continuing to use Apple's gcc.
>>> If you are trying to compile with homebrew's llvm, you should probably 
>>> configure by setting CC and CXX as well. But this is also untested - I have 
>>> created https://trac.sagemath.org/ticket/30835#ticket for testing such 
>>> a configuration.
>>>
>>>
>>> On Tuesday, October 27, 2020 at 3:46:10 AM UTC-7, Dima Pasechnik wrote:
>>>
 I'd have tried removing llvm and trying again. Perhaps this is a 
 conflict between Homebrew packages.

 On Tue, Oct 27, 2020 at 8:42 AM modp...@gmail.com  
 wrote:

>>> Please find config.log and cysignals-1.10.2.log attached. I already run 
> "source .homebrew-build-env" before configuring.
> And yes I also have llvm installed through Homebrew.
>
> On Monday, October 26, 2020 at 3:23:38 PM UTC+1 dim...@gmail.com 
> wrote:
>
>> also note that you apparently have something in 
>> -L/usr/local/opt/llvm/lib (installed from Homebrew ?) which might 
>> lead 
>> to surprises. 
>> Do you have some LDFLAGS set? 
>> It would help if you also post logs/pkgs/cysignals-1.10.2.log 
>>
>> On Mon, Oct 26, 2020 at 2:15 PM Dima Pasechnik  
>> wrote: 
>> > 
>> > also, if you have Homebrew, you should run 
>> > 
>> > source .homebrew-build-env 
>> > 
>> > before 
>> > 
>> > ./configure 
>> > 
>> > On Mon, Oct 26, 2020 at 1:50 PM Dima Pasechnik  
>> wrote: 
>> >> 
>> >> please post the top-level config.log here 
>> >> 
>> >> On Mon, 26 Oct 2020, 13:45 modp...@gmail.com,  
>> wrote: 
>> >>> 
>> >>> 
>> >>> I'm building Sage 9.2 from source on macOS Catalina 10.15.7, 
>> however, it fails 
>> >>> when trying to install cysignals. More precisely, it throws the 
>> following error: 
>> >>> 
>> >>> gcc -bundle -undefined dynamic_lookup -isysroot 
>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
>>  
>> -L/Users/myUser/app/sage-9.2/local/lib 
>> -Wl,-rpath,/Users/myUser/app/sage-9.2/local/lib 
>> -L/usr/local/opt/llvm/lib 
>> -I/usr/local/opt/llvm/include -Wp,-U_FORTIFY_SOURCE 
>> build/temp.macosx-10.15-x86_64-3.8/build/src/cysignals/signals.o 
>> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib 
>> -L/usr/local/opt/sqlite/lib -o 
>> build/lib.macosx-10.15-x86_64-3.8/cysignals/
>> signals.cpython-38-darwin.so -lpari -pthread 
>> >>> ld: illegal thread local variable reference to regular symbol 
>> _PARI_SIGINT_block for architecture x86_64 
>> >>> clang: error: linker command failed with exit code 1 (use -v to 
>> see invocation) 
>> >>> error: 

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

Hi Isuru,

   Thank you so much.  I missed your message yesterday, but I also asked on 
their forum and they made the same suggestion and said it would be fixed in 
3.11. I still asked the homebrew people to add a TARGET to their builds so 
hopefully that will get straightened out as well.

On Monday, October 12, 2020 at 11:04:41 PM UTC-4 isu...@gmail.com wrote:

> Hi Zachary,
>
> You might be hitting https://github.com/xianyi/OpenBLAS/issues/2728 which 
> is fixed in https://github.com/xianyi/OpenBLAS/pull/2729 but not in 
> 0.3.10.
>
> Isuru
>
> On Mon, Oct 12, 2020 at 10:01 PM Zachary Scherr  wrote:
>
>> Hi Isuru,
>>
>>I've been trying to fix homebrew's openblas, and I'm running into an 
>> issue that I was hoping you might know something about.  If I build 
>> openBLAS with TARGET=HASWELL then I don't have any issues with numpy.  
>> However, if I build it with TARGET=NEHALEM, which is what they want for 
>> homebrew, then I still run into the same numpy error.  I see that 
>> Conda-forge uses TARGET=PRESCOTT, but if I try that I also run into the 
>> same numpy problem.  Do you have any insight into why this might be the 
>> case?
>>
>> Thanks,
>> Zach
>>
>> On Monday, October 12, 2020 at 4:14:28 PM UTC-4 Zachary Scherr wrote:
>>
>>> Ah, thank you.  I'll post the issue and see if I can get homebrew to 
>>> resolve it!
>>>
>>> On Monday, October 12, 2020 at 2:29:10 PM UTC-4 isu...@gmail.com wrote:
>>>
>>>> You don't need different TARGETs. `DYNAMIC_ARCH=1` means that it will 
>>>> detect at runtime what the CPU is and will use the kernel matching the CPU 
>>>> at runtime. `TARGET` gives the oldest CPU that this code will run on so 
>>>> that the common code is compiled to target this.
>>>>
>>>> Isuru
>>>>
>>>> On Mon, Oct 12, 2020 at 1:24 PM Zachary Scherr  
>>>> wrote:
>>>>
>>>>> I posted about it on their discussion page, but I'm not sure there 
>>>>> will be anything they can do.  They build their libraries on several 
>>>>> different versions of MacOS, but I'm not sure they build with several 
>>>>> different TARGETS.  I can try to pursue this, but the easy fix for now is 
>>>>> that if people want to install openblas via homebrew they should install 
>>>>> from source.
>>>>>
>>>>> On Monday, October 12, 2020 at 2:09:28 PM UTC-4 dim...@gmail.com 
>>>>> wrote:
>>>>>
>>>>>> On Mon, Oct 12, 2020 at 6:17 PM Isuru Fernando  
>>>>>> wrote: 
>>>>>> > 
>>>>>> > I looked at the openblas formula in homebrew and they are not 
>>>>>> passing the TARGET option. When using DYNAMIC_ARCH=1, a target should be 
>>>>>> specified. 
>>>>>>
>>>>>> care to open an issue with them on 
>>>>>> https://github.com/Homebrew/homebrew-core ? 
>>>>>>
>>>>>> > 
>>>>>> > Isuru 
>>>>>> > 
>>>>>> > On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr  
>>>>>> wrote: 
>>>>>> >> 
>>>>>> >> In case anyone is curious, I've tracked the problem down to 
>>>>>> homebrew's openBLAS and so it has nothing to do with sage. If I build 
>>>>>> numpy 
>>>>>> from source through homebrew then I get exactly the same error using my 
>>>>>> system python3. I'm wondering if maybe this has something to do with the 
>>>>>> fact that openBLAS is bottled with a different processor type than the 
>>>>>> one 
>>>>>> that is on my system. In any case I'll ask over there and see if I can 
>>>>>> get 
>>>>>> some help. 
>>>>>> >> 
>>>>>> >> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr 
>>>>>> wrote: 
>>>>>> >>> 
>>>>>> >>> Hi Dima, 
>>>>>> >>> 
>>>>>> >>> My system-wide numpy is installed via pip. I was just remarking 
>>>>>> that I didn't build my system-wide numpy from source so it's not a fair 
>>>>>> comparison. It's possible that the issues aren't sage related but are 
>>>>>> related to building sage's numpy against some homebrew libraries. 
>>>>>> >>> 
>>&

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

Hi Isuru,

   I've been trying to fix homebrew's openblas, and I'm running into an 
issue that I was hoping you might know something about.  If I build 
openBLAS with TARGET=HASWELL then I don't have any issues with numpy. 
 However, if I build it with TARGET=NEHALEM, which is what they want for 
homebrew, then I still run into the same numpy error.  I see that 
Conda-forge uses TARGET=PRESCOTT, but if I try that I also run into the 
same numpy problem.  Do you have any insight into why this might be the 
case?

Thanks,
Zach

On Monday, October 12, 2020 at 4:14:28 PM UTC-4 Zachary Scherr wrote:

> Ah, thank you.  I'll post the issue and see if I can get homebrew to 
> resolve it!
>
> On Monday, October 12, 2020 at 2:29:10 PM UTC-4 isu...@gmail.com wrote:
>
>> You don't need different TARGETs. `DYNAMIC_ARCH=1` means that it will 
>> detect at runtime what the CPU is and will use the kernel matching the CPU 
>> at runtime. `TARGET` gives the oldest CPU that this code will run on so 
>> that the common code is compiled to target this.
>>
>> Isuru
>>
>> On Mon, Oct 12, 2020 at 1:24 PM Zachary Scherr  wrote:
>>
>>> I posted about it on their discussion page, but I'm not sure there will 
>>> be anything they can do.  They build their libraries on several different 
>>> versions of MacOS, but I'm not sure they build with several different 
>>> TARGETS.  I can try to pursue this, but the easy fix for now is that if 
>>> people want to install openblas via homebrew they should install from 
>>> source.
>>>
>>> On Monday, October 12, 2020 at 2:09:28 PM UTC-4 dim...@gmail.com wrote:
>>>
>>>> On Mon, Oct 12, 2020 at 6:17 PM Isuru Fernando  
>>>> wrote: 
>>>> > 
>>>> > I looked at the openblas formula in homebrew and they are not passing 
>>>> the TARGET option. When using DYNAMIC_ARCH=1, a target should be 
>>>> specified. 
>>>>
>>>> care to open an issue with them on 
>>>> https://github.com/Homebrew/homebrew-core ? 
>>>>
>>>> > 
>>>> > Isuru 
>>>> > 
>>>> > On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr  
>>>> wrote: 
>>>> >> 
>>>> >> In case anyone is curious, I've tracked the problem down to 
>>>> homebrew's openBLAS and so it has nothing to do with sage. If I build 
>>>> numpy 
>>>> from source through homebrew then I get exactly the same error using my 
>>>> system python3. I'm wondering if maybe this has something to do with the 
>>>> fact that openBLAS is bottled with a different processor type than the one 
>>>> that is on my system. In any case I'll ask over there and see if I can get 
>>>> some help. 
>>>> >> 
>>>> >> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr 
>>>> wrote: 
>>>> >>> 
>>>> >>> Hi Dima, 
>>>> >>> 
>>>> >>> My system-wide numpy is installed via pip. I was just remarking 
>>>> that I didn't build my system-wide numpy from source so it's not a fair 
>>>> comparison. It's possible that the issues aren't sage related but are 
>>>> related to building sage's numpy against some homebrew libraries. 
>>>> >>> 
>>>> >>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com 
>>>> wrote: 
>>>> >>>> 
>>>> >>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr  
>>>> wrote: 
>>>> >>>> > 
>>>> >>>> > That also crashes with: 86622 segmentation fault ./sage --python 
>>>> >>>> > 
>>>> >>>> > I tested this both with building sage against homebrew python 
>>>> 3.8.6 and against sage's default python 3.8.5 and the same error occurred 
>>>> in both cases. I don't have this problem using my system-wide numpy so 
>>>> it's 
>>>> possible that because sage numpy is built from source that maybe one of my 
>>>> homebrew libraries is causing issues. I found 
>>>> https://github.com/numpy/numpy/issues/11551 which could be relevant 
>>>> and might indicate that it's not a sage problem. 
>>>> >>>> 
>>>> >>>> If you are talking about Homebrew's numpy, it should be more or 
>>>> less 
>>>> >>>> identical with Sage's numpy (assuming you use Homebrew's openbla

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

Ah, thank you.  I'll post the issue and see if I can get homebrew to 
resolve it!

On Monday, October 12, 2020 at 2:29:10 PM UTC-4 isu...@gmail.com wrote:

> You don't need different TARGETs. `DYNAMIC_ARCH=1` means that it will 
> detect at runtime what the CPU is and will use the kernel matching the CPU 
> at runtime. `TARGET` gives the oldest CPU that this code will run on so 
> that the common code is compiled to target this.
>
> Isuru
>
> On Mon, Oct 12, 2020 at 1:24 PM Zachary Scherr  wrote:
>
>> I posted about it on their discussion page, but I'm not sure there will 
>> be anything they can do.  They build their libraries on several different 
>> versions of MacOS, but I'm not sure they build with several different 
>> TARGETS.  I can try to pursue this, but the easy fix for now is that if 
>> people want to install openblas via homebrew they should install from 
>> source.
>>
>> On Monday, October 12, 2020 at 2:09:28 PM UTC-4 dim...@gmail.com wrote:
>>
>>> On Mon, Oct 12, 2020 at 6:17 PM Isuru Fernando  
>>> wrote: 
>>> > 
>>> > I looked at the openblas formula in homebrew and they are not passing 
>>> the TARGET option. When using DYNAMIC_ARCH=1, a target should be specified. 
>>>
>>> care to open an issue with them on 
>>> https://github.com/Homebrew/homebrew-core ? 
>>>
>>> > 
>>> > Isuru 
>>> > 
>>> > On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr  
>>> wrote: 
>>> >> 
>>> >> In case anyone is curious, I've tracked the problem down to 
>>> homebrew's openBLAS and so it has nothing to do with sage. If I build numpy 
>>> from source through homebrew then I get exactly the same error using my 
>>> system python3. I'm wondering if maybe this has something to do with the 
>>> fact that openBLAS is bottled with a different processor type than the one 
>>> that is on my system. In any case I'll ask over there and see if I can get 
>>> some help. 
>>> >> 
>>> >> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr 
>>> wrote: 
>>> >>> 
>>> >>> Hi Dima, 
>>> >>> 
>>> >>> My system-wide numpy is installed via pip. I was just remarking that 
>>> I didn't build my system-wide numpy from source so it's not a fair 
>>> comparison. It's possible that the issues aren't sage related but are 
>>> related to building sage's numpy against some homebrew libraries. 
>>> >>> 
>>> >>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com 
>>> wrote: 
>>> >>>> 
>>> >>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr  
>>> wrote: 
>>> >>>> > 
>>> >>>> > That also crashes with: 86622 segmentation fault ./sage --python 
>>> >>>> > 
>>> >>>> > I tested this both with building sage against homebrew python 
>>> 3.8.6 and against sage's default python 3.8.5 and the same error occurred 
>>> in both cases. I don't have this problem using my system-wide numpy so it's 
>>> possible that because sage numpy is built from source that maybe one of my 
>>> homebrew libraries is causing issues. I found 
>>> https://github.com/numpy/numpy/issues/11551 which could be relevant and 
>>> might indicate that it's not a sage problem. 
>>> >>>> 
>>> >>>> If you are talking about Homebrew's numpy, it should be more or 
>>> less 
>>> >>>> identical with Sage's numpy (assuming you use Homebrew's openblas 
>>> in 
>>> >>>> Sage) 
>>> >>>> cf. 
>>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb 
>>> >>>> 
>>> >>>> > 
>>> >>>> > I should also add that if I lower the dimension of x to 10 
>>> then it works without problem. 
>>> >>>> > 
>>> >>>> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com 
>>> wrote: 
>>> >>>> >> 
>>> >>>> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr  
>>> wrote: 
>>> >>>> >> > 
>>> >>>> >> > Hi All, 
>>> >>>> >> > 
>>> >>>> >> > I was doing some bug hunting and noticed that scipy's pytests 
>>> crashed pretty early. I track

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

I posted about it on their discussion page, but I'm not sure there will be 
anything they can do.  They build their libraries on several different 
versions of MacOS, but I'm not sure they build with several different 
TARGETS.  I can try to pursue this, but the easy fix for now is that if 
people want to install openblas via homebrew they should install from 
source.

On Monday, October 12, 2020 at 2:09:28 PM UTC-4 dim...@gmail.com wrote:

> On Mon, Oct 12, 2020 at 6:17 PM Isuru Fernando  wrote:
> >
> > I looked at the openblas formula in homebrew and they are not passing 
> the TARGET option. When using DYNAMIC_ARCH=1, a target should be specified.
>
> care to open an issue with them on 
> https://github.com/Homebrew/homebrew-core ?
>
> >
> > Isuru
> >
> > On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr  
> wrote:
> >>
> >> In case anyone is curious, I've tracked the problem down to homebrew's 
> openBLAS and so it has nothing to do with sage. If I build numpy from 
> source through homebrew then I get exactly the same error using my system 
> python3. I'm wondering if maybe this has something to do with the fact that 
> openBLAS is bottled with a different processor type than the one that is on 
> my system. In any case I'll ask over there and see if I can get some help.
> >>
> >> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr wrote:
> >>>
> >>> Hi Dima,
> >>>
> >>> My system-wide numpy is installed via pip. I was just remarking that I 
> didn't build my system-wide numpy from source so it's not a fair 
> comparison. It's possible that the issues aren't sage related but are 
> related to building sage's numpy against some homebrew libraries.
> >>>
> >>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com 
> wrote:
> >>>>
> >>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr  
> wrote:
> >>>> >
> >>>> > That also crashes with: 86622 segmentation fault ./sage --python
> >>>> >
> >>>> > I tested this both with building sage against homebrew python 3.8.6 
> and against sage's default python 3.8.5 and the same error occurred in both 
> cases. I don't have this problem using my system-wide numpy so it's 
> possible that because sage numpy is built from source that maybe one of my 
> homebrew libraries is causing issues. I found 
> https://github.com/numpy/numpy/issues/11551 which could be relevant and 
> might indicate that it's not a sage problem.
> >>>>
> >>>> If you are talking about Homebrew's numpy, it should be more or less
> >>>> identical with Sage's numpy (assuming you use Homebrew's openblas in
> >>>> Sage)
> >>>> cf. 
> https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb
> >>>>
> >>>> >
> >>>> > I should also add that if I lower the dimension of x to 10 then 
> it works without problem.
> >>>> >
> >>>> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com 
> wrote:
> >>>> >>
> >>>> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr  
> wrote:
> >>>> >> >
> >>>> >> > Hi All,
> >>>> >> >
> >>>> >> > I was doing some bug hunting and noticed that scipy's pytests 
> crashed pretty early. I tracked down exactly what was causing the problem 
> and noticed it can be reproduced by the following sequence of commands:
> >>>> >> >
> >>>> >> > sage: import numpy as np
> >>>> >> > sage: x = np.random.randn(100,2)
> >>>> >> > sage: y = np.random.randn(2,2)
> >>>> >> > sage: x.dot(y)
> >>>> >>
> >>>> >> please test this in "plain" Sage python, i.e. does
> >>>> >>
> >>>> >> ./sage --python
> >>>> >>
> >>>> >> >>> import numpy as np
> >>>> >> >>> x = np.random.randn(100,2)
> >>>> >> >>> y = np.random.randn(2,2)
> >>>> >> >>> x.dot(y)
> >>>> >>
> >>>> >> reproduce the crash?
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >> >
> >>>> >> > produces:
> >>>> >> >
> >>>> >> > 
> -

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

Aha.  In fact, if I do

brew install openblas --build-from-source

then it picks up the TARGET automatically and I don't have any problems 
with numpy whatsoever.  I'll still ask over there, but I'm guessing this is 
the problem with trying to use bottled versions of the libraries.
On Monday, October 12, 2020 at 1:17:30 PM UTC-4 isu...@gmail.com wrote:

> I looked at the openblas formula in homebrew and they are not passing the 
> TARGET option. When using DYNAMIC_ARCH=1, a target should be specified.
>
> Isuru
>
> On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr  wrote:
>
>> In case anyone is curious, I've tracked the problem down to homebrew's 
>> openBLAS and so it has nothing to do with sage.  If I build numpy from 
>> source through homebrew then I get exactly the same error using my system 
>> python3.  I'm wondering if maybe this has something to do with the fact 
>> that openBLAS is bottled with a different processor type than the one that 
>> is on my system.  In any case I'll ask over there and see if I can get some 
>> help.
>>
>> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr wrote:
>>
>>> Hi Dima,
>>>
>>>My system-wide numpy is installed via pip.  I was just remarking that 
>>> I didn't build my system-wide numpy from source so it's not a fair 
>>> comparison.  It's possible that the issues aren't sage related but are 
>>> related to building sage's numpy against some homebrew libraries.
>>>
>>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com wrote:
>>>
>>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr  
>>>> wrote: 
>>>> > 
>>>> > That also crashes with: 86622 segmentation fault ./sage --python 
>>>> > 
>>>> > I tested this both with building sage against homebrew python 3.8.6 
>>>> and against sage's default python 3.8.5 and the same error occurred in 
>>>> both 
>>>> cases. I don't have this problem using my system-wide numpy so it's 
>>>> possible that because sage numpy is built from source that maybe one of my 
>>>> homebrew libraries is causing issues. I found 
>>>> https://github.com/numpy/numpy/issues/11551 which could be relevant 
>>>> and might indicate that it's not a sage problem. 
>>>>
>>>> If you are talking about Homebrew's numpy, it should be more or less 
>>>> identical with Sage's numpy (assuming you use Homebrew's openblas in 
>>>> Sage) 
>>>> cf. 
>>>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb 
>>>>
>>>> > 
>>>> > I should also add that if I lower the dimension of x to 10 then 
>>>> it works without problem. 
>>>> > 
>>>> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com 
>>>> wrote: 
>>>> >> 
>>>> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr  
>>>> wrote: 
>>>> >> > 
>>>> >> > Hi All, 
>>>> >> > 
>>>> >> > I was doing some bug hunting and noticed that scipy's pytests 
>>>> crashed pretty early. I tracked down exactly what was causing the problem 
>>>> and noticed it can be reproduced by the following sequence of commands: 
>>>> >> > 
>>>> >> > sage: import numpy as np 
>>>> >> > sage: x = np.random.randn(100,2) 
>>>> >> > sage: y = np.random.randn(2,2) 
>>>> >> > sage: x.dot(y) 
>>>> >> 
>>>> >> please test this in "plain" Sage python, i.e. does 
>>>> >> 
>>>> >> ./sage --python 
>>>> >> 
>>>> >> >>> import numpy as np 
>>>> >> >>> x = np.random.randn(100,2) 
>>>> >> >>> y = np.random.randn(2,2) 
>>>> >> >>> x.dot(y) 
>>>> >> 
>>>> >> reproduce the crash? 
>>>> >> 
>>>> >> 
>>>> >> 
>>>> >> > 
>>>> >> > produces: 
>>>> >> > 
>>>> >> > 
>>>>  
>>>> >> > 0 signals.cpython-38-darwin.so 0x0001088bc62a print_backtrace 
>>>> + 58 
>>>> >> > 1 signals.cpython-38-darwin.so 0x0001088c0277 sigdie + 39 
>>>

Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

In case anyone is curious, I've tracked the problem down to homebrew's 
openBLAS and so it has nothing to do with sage.  If I build numpy from 
source through homebrew then I get exactly the same error using my system 
python3.  I'm wondering if maybe this has something to do with the fact 
that openBLAS is bottled with a different processor type than the one that 
is on my system.  In any case I'll ask over there and see if I can get some 
help.

On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr wrote:

> Hi Dima,
>
>My system-wide numpy is installed via pip.  I was just remarking that I 
> didn't build my system-wide numpy from source so it's not a fair 
> comparison.  It's possible that the issues aren't sage related but are 
> related to building sage's numpy against some homebrew libraries.
>
> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com wrote:
>
>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr  wrote:
>> >
>> > That also crashes with: 86622 segmentation fault ./sage --python
>> >
>> > I tested this both with building sage against homebrew python 3.8.6 and 
>> against sage's default python 3.8.5 and the same error occurred in both 
>> cases. I don't have this problem using my system-wide numpy so it's 
>> possible that because sage numpy is built from source that maybe one of my 
>> homebrew libraries is causing issues. I found 
>> https://github.com/numpy/numpy/issues/11551 which could be relevant and 
>> might indicate that it's not a sage problem.
>>
>> If you are talking about Homebrew's numpy, it should be more or less
>> identical with Sage's numpy (assuming you use Homebrew's openblas in
>> Sage)
>> cf. 
>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb
>>
>> >
>> > I should also add that if I lower the dimension of x to 100000 then it 
>> works without problem.
>> >
>> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com wrote:
>> >>
>> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr  
>> wrote:
>> >> >
>> >> > Hi All,
>> >> >
>> >> > I was doing some bug hunting and noticed that scipy's pytests 
>> crashed pretty early. I tracked down exactly what was causing the problem 
>> and noticed it can be reproduced by the following sequence of commands:
>> >> >
>> >> > sage: import numpy as np
>> >> > sage: x = np.random.randn(100,2)
>> >> > sage: y = np.random.randn(2,2)
>> >> > sage: x.dot(y)
>> >>
>> >> please test this in "plain" Sage python, i.e. does
>> >>
>> >> ./sage --python
>> >>
>> >> >>> import numpy as np
>> >> >>> x = np.random.randn(100,2)
>> >> >>> y = np.random.randn(2,2)
>> >> >>> x.dot(y)
>> >>
>> >> reproduce the crash?
>> >>
>> >>
>> >>
>> >> >
>> >> > produces:
>> >> >
>> >> > 
>> 
>> >> > 0 signals.cpython-38-darwin.so 0x0001088bc62a print_backtrace + 
>> 58
>> >> > 1 signals.cpython-38-darwin.so 0x0001088c0277 sigdie + 39
>> >> > 2 signals.cpython-38-darwin.so 0x0001088c0212 sigdie_for_sig + 
>> 290
>> >> > 3 libsystem_platform.dylib 0x7fff6c88e5fd _sigtramp + 29
>> >> > 
>> 
>> >> > Unhandled SIGBUS: A bus error occurred.
>> >> > This probably occurred because a *compiled* module has a bug
>> >> > in it and is not properly wrapped with sig_on(), sig_off().
>> >> > Python will now terminate.
>> >> > 
>> 
>> >> > /Users/zscherr/sage/src/bin/sage-python: line 2: 78812 Bus error: 10 
>> sage -python "$@"
>> >> >
>> >> > I haven't tested on any other platforms, but for what it's worth I 
>> have Catalina 10.15.7 with Xcode 12.
>> >> >
>> >> > Thanks,
>> >> > Zach
>> >> >
>> >> > --
>> >> > 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/28f58136-d3c7-40b7-9a46-36fc347acc2en%40googlegroups.com
>> .
>> >
>> > --
>> > 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/a67ca4b5-526b-40d7-a476-520d49890207n%40googlegroups.com
>> .
>>
>

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Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

Hi Dima,

   My system-wide numpy is installed via pip.  I was just remarking that I 
didn't build my system-wide numpy from source so it's not a fair 
comparison.  It's possible that the issues aren't sage related but are 
related to building sage's numpy against some homebrew libraries.

On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com wrote:

> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr  wrote:
> >
> > That also crashes with: 86622 segmentation fault ./sage --python
> >
> > I tested this both with building sage against homebrew python 3.8.6 and 
> against sage's default python 3.8.5 and the same error occurred in both 
> cases. I don't have this problem using my system-wide numpy so it's 
> possible that because sage numpy is built from source that maybe one of my 
> homebrew libraries is causing issues. I found 
> https://github.com/numpy/numpy/issues/11551 which could be relevant and 
> might indicate that it's not a sage problem.
>
> If you are talking about Homebrew's numpy, it should be more or less
> identical with Sage's numpy (assuming you use Homebrew's openblas in
> Sage)
> cf. https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb
>
> >
> > I should also add that if I lower the dimension of x to 10 then it 
> works without problem.
> >
> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com wrote:
> >>
> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr  
> wrote:
> >> >
> >> > Hi All,
> >> >
> >> > I was doing some bug hunting and noticed that scipy's pytests crashed 
> pretty early. I tracked down exactly what was causing the problem and 
> noticed it can be reproduced by the following sequence of commands:
> >> >
> >> > sage: import numpy as np
> >> > sage: x = np.random.randn(100,2)
> >> > sage: y = np.random.randn(2,2)
> >> > sage: x.dot(y)
> >>
> >> please test this in "plain" Sage python, i.e. does
> >>
> >> ./sage --python
> >>
> >> >>> import numpy as np
> >> >>> x = np.random.randn(100,2)
> >> >>> y = np.random.randn(2,2)
> >> >>> x.dot(y)
> >>
> >> reproduce the crash?
> >>
> >>
> >>
> >> >
> >> > produces:
> >> >
> >> > 
> 
> >> > 0 signals.cpython-38-darwin.so 0x0001088bc62a print_backtrace + 
> 58
> >> > 1 signals.cpython-38-darwin.so 0x0001088c0277 sigdie + 39
> >> > 2 signals.cpython-38-darwin.so 0x0001088c0212 sigdie_for_sig + 
> 290
> >> > 3 libsystem_platform.dylib 0x7fff6c88e5fd _sigtramp + 29
> >> > 
> 
> >> > Unhandled SIGBUS: A bus error occurred.
> >> > This probably occurred because a *compiled* module has a bug
> >> > in it and is not properly wrapped with sig_on(), sig_off().
> >> > Python will now terminate.
> >> > 
> 
> >> > /Users/zscherr/sage/src/bin/sage-python: line 2: 78812 Bus error: 10 
> sage -python "$@"
> >> >
> >> > I haven't tested on any other platforms, but for what it's worth I 
> have Catalina 10.15.7 with Xcode 12.
> >> >
> >> > Thanks,
> >> > Zach
> >> >
> >> > --
> >> > 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/28f58136-d3c7-40b7-9a46-36fc347acc2en%40googlegroups.com
> .
> >
> > --
> > 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/a67ca4b5-526b-40d7-a476-520d49890207n%40googlegroups.com
> .
>

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Re: [sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

That also crashes with: 86622 segmentation fault  ./sage --python

I tested this both with building sage against homebrew python 3.8.6 and 
against sage's default python 3.8.5 and the same error occurred in both 
cases.  I don't have this problem using my system-wide numpy so it's 
possible that because sage numpy is built from source that maybe one of my 
homebrew libraries is causing issues.  I 
found https://github.com/numpy/numpy/issues/11551 which could be relevant 
and might indicate that it's not a sage problem.

I should also add that if I lower the dimension of x to 10 then it 
works without problem.

On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 dim...@gmail.com wrote:

> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr  wrote:
> >
> > Hi All,
> >
> > I was doing some bug hunting and noticed that scipy's pytests crashed 
> pretty early. I tracked down exactly what was causing the problem and 
> noticed it can be reproduced by the following sequence of commands:
> >
> > sage: import numpy as np
> > sage: x = np.random.randn(100,2)
> > sage: y = np.random.randn(2,2)
> > sage: x.dot(y)
>
> please test this in "plain" Sage python, i.e. does
>
> ./sage --python
>
> >>> import numpy as np
> >>> x = np.random.randn(100,2)
> >>> y = np.random.randn(2,2)
> >>> x.dot(y)
>
> reproduce the crash?
>
>
>
> >
> > produces:
> >
> > 
> > 0 signals.cpython-38-darwin.so 0x0001088bc62a print_backtrace + 58
> > 1 signals.cpython-38-darwin.so 0x0001088c0277 sigdie + 39
> > 2 signals.cpython-38-darwin.so 0x0001088c0212 sigdie_for_sig + 290
> > 3 libsystem_platform.dylib 0x7fff6c88e5fd _sigtramp + 29
> > 
> > Unhandled SIGBUS: A bus error occurred.
> > This probably occurred because a *compiled* module has a bug
> > in it and is not properly wrapped with sig_on(), sig_off().
> > Python will now terminate.
> > 
> > /Users/zscherr/sage/src/bin/sage-python: line 2: 78812 Bus error: 10 
> sage -python "$@"
> >
> > I haven't tested on any other platforms, but for what it's worth I have 
> Catalina 10.15.7 with Xcode 12.
> >
> > Thanks,
> > Zach
> >
> > --
> > 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.
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> https://groups.google.com/d/msgid/sage-devel/28f58136-d3c7-40b7-9a46-36fc347acc2en%40googlegroups.com
> .
>

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[sage-devel] Numpy crashing on sage 9.2.RC0

[Zachary Scherr]

Hi All,

   I was doing some bug hunting and noticed that scipy's pytests crashed 
pretty early.  I tracked down exactly what was causing the problem and 
noticed it can be reproduced by the following sequence of commands:

sage: import numpy as np
sage: x = np.random.randn(100,2)
sage: y = np.random.randn(2,2)
sage: x.dot(y)

produces:


0   signals.cpython-38-darwin.so0x0001088bc62a print_backtrace 
+ 58
1   signals.cpython-38-darwin.so0x0001088c0277 sigdie + 39
2   signals.cpython-38-darwin.so0x0001088c0212 sigdie_for_sig + 
290
3   libsystem_platform.dylib0x7fff6c88e5fd _sigtramp + 29

Unhandled SIGBUS: A bus error occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.

/Users/zscherr/sage/src/bin/sage-python: line 2: 78812 Bus error: 10   
sage -python "$@"

I haven't tested on any other platforms, but for what it's worth I have 
Catalina 10.15.7 with Xcode 12.

Thanks,
Zach

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Re: [sage-devel] Re: Beta 12 not building (Homebrew singular issue?)

[Zachary Scherr]

Thank you Matthias.  I think I've learned my lesson about over installing 
homebrew packages.  I previously installed every single homebrew version of 
all Sage SPKGs in case I could speed up build time.  At some point I'd like 
to learn more about the sage build process so that I can contribute in 
fixing my own issues.

On Thursday, October 8, 2020 at 12:13:31 PM UTC-4 Matthias Koeppe wrote:

> I have opened https://trac.sagemath.org/ticket/30745 for this and the 
> other error with ecl, which I think have a common cause. 
>
>
> On Wednesday, October 7, 2020 at 7:33:32 AM UTC-7, Zachary Scherr wrote:
>>
>> I was just curious as to what the status of this issue is, and if there 
>> was anything I could do to help with review.  I can build rc0 using Dima's 
>> suggested spkg-configure.m4 fix, but I can't build it otherwise unless I 
>> brew unlink singular first. 
>>
>> On Friday, September 11, 2020 at 6:47:23 PM UTC-4 dim...@gmail.com wrote:
>>
>>> as an experiment, I hardcoded the necessary paths for using Homebrew's 
>>> Singular here:
>>>
>>> https://trac.sagemath.org/attachment/ticket/29024/homebrew-singular-experiment.patch
>>> (the part for  src/sage/libs/singular/singular.pxd is probably not 
>>> needed, but anyway)
>>>
>>> running tests now.
>>>
>>> On Fri, Sep 11, 2020 at 6:15 PM Dima Pasechnik  wrote:
>>>
>>>>
>>>>
>>>> On Fri, Sep 11, 2020 at 3:32 PM Dima Pasechnik  
>>>> wrote:
>>>>
>>>>> I think there is at least one place elsewhere in the code that assumes 
>>>>> that Singular is installed in $SAGE_LOCAL
>>>>>
>>>>> at least I got an error of this sort while trying to build Sage's docs 
>>>>> in this configuration.
>>>>> I'll look into it once back at the keyboard
>>>>>
>>>>
>>>> this problem is explained in 
>>>> https://trac.sagemath.org/ticket/29024#comment:8
>>>>
>>>> The fix needs some programming - specifically, the code in singular.pyx 
>>>> calls dlopen on SINGULAR_SO,
>>>> which is computed by _get_shared_lib_filename dynamically in env.py, 
>>>> and assuming that it is in SAGE_LOCAL.
>>>> So this probably can instead by handled using cython_aliases from the 
>>>> same module (which does compute
>>>> all the needed info for Singular, it seems).
>>>> Or by fixing _get_shared_lib_filename so that it also searches 
>>>> elsewhere.
>>>>
>>>>
>>>>> On Fri, 11 Sep 2020, 15:10 Zachary Scherr,  wrote:
>>>>>
>>>>>> Hi Dima,
>>>>>>
>>>>>>Thanks! Downloading spkg-configure.m4 allowed me to build 
>>>>>> successfully.
>>>>>>
>>>>>> Best,
>>>>>> Zach
>>>>>>
>>>>>> On Friday, September 11, 2020 at 5:45:00 AM UTC-4 dim...@gmail.com 
>>>>>> wrote:
>>>>>>
>>>>>>> On Fri, Sep 11, 2020 at 10:11 AM Dima Pasechnik  
>>>>>>> wrote:
>>>>>>>
>>>>>>>> [sagelib-9.2.beta12] installing. Log file: 
>>>>>>>> /Users/zscherr/sage/develop/logs/pkgs/sagelib-9.2.beta12.log
>>>>>>>>   [sagelib-9.2.beta12] error installing, exit status 1. End of log 
>>>>>>>> file:
>>>>>>>>   [sagelib-9.2.beta12]   
>>>>>>>> /usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 
>>>>>>>> 'polys/shiftop.h' file not found
>>>>>>>>   [sagelib-9.2.beta12]   #include "polys/shiftop.h"
>>>>>>>>   [sagelib-9.2.beta12]^
>>>>>>>>
>>>>>>>> the include path looks funny with its "singular/Singular/"
>>>>>>>> I don't know what brew does here, maybe it drops "singular/" bit?
>>>>>>>>
>>>>>>>
>>>>>>> no, in fact it's all fine, it's just include flags that need to be 
>>>>>>> adjusted.
>>>>>>> Note that you still have 
>>>>>>> -I/Users/zscherr/sage/develop/local/include/singular
>>>>>>> in the failing gcc call, which seems to indicate you didn't use
>>>>>>>
>>>>>>> https://trac.sagemath.org/attachment/ticket/29024/s

[sage-devel] Re: make doc fails on manifolds

[Zachary Scherr]

Yes, through Homebrew.  I'll unlink it tomorrow and I'm guessing that'll 
fix the problem.  Thanks, I got confused because it looked like it was 
grabbing it from my sage folder and not /usr/local, but I didn't notice ECL 
being built.

On Wednesday, October 7, 2020 at 11:09:19 PM UTC-4 Matthias Koeppe wrote:

> On Wednesday, October 7, 2020 at 4:42:23 PM UTC-7, Zachary Scherr wrote:
>>
>>I was building sage today, and the building of sage seems to work fine 
>> but building the documentation crashed for me at manifolds.  Does anyone 
>> have any insight as to what's going on?
>>
>
> From the log:
>
> 
> [manifolds] from sage.libs.ecl import EclObject, ecl_eval
> [manifolds] ImportError: 
> dlopen(/Users/zscherr/sage/local/lib/python3.8/site-packages/sage/libs/ecl.cpython-38-darwin.so,
>  2): Symbol not found: _ecl_process_env
> [manifolds]   Referenced from: 
> /Users/zscherr/sage/local/lib/python3.8/site-packages/sage/libs/ecl.cpython-38-darwin.so
> [manifolds]   Expected in: flat namespace
>
>
> Do you have another installation of ecl, perhaps in /usr/local?  In that 
> case, this problem may have a similar cause as the problems related to 
> ntl/flint that you reported earlier.
>  
>

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Re: [sage-devel] Re: Beta 12 not building (Homebrew singular issue?)

[Zachary Scherr]

I should probably also add that while sage builds with 
the spkg-configure.m4 fix, my documentation will not build unless I brew 
unlink singular.

On Wednesday, October 7, 2020 at 10:33:32 AM UTC-4 Zachary Scherr wrote:

> I was just curious as to what the status of this issue is, and if there 
> was anything I could do to help with review.  I can build rc0 using Dima's 
> suggested spkg-configure.m4 fix, but I can't build it otherwise unless I 
> brew unlink singular first. 
>
> On Friday, September 11, 2020 at 6:47:23 PM UTC-4 dim...@gmail.com wrote:
>
>> as an experiment, I hardcoded the necessary paths for using Homebrew's 
>> Singular here:
>>
>> https://trac.sagemath.org/attachment/ticket/29024/homebrew-singular-experiment.patch
>> (the part for  src/sage/libs/singular/singular.pxd is probably not 
>> needed, but anyway)
>>
>> running tests now.
>>
>> On Fri, Sep 11, 2020 at 6:15 PM Dima Pasechnik  wrote:
>>
>>>
>>>
>>> On Fri, Sep 11, 2020 at 3:32 PM Dima Pasechnik  wrote:
>>>
>>>> I think there is at least one place elsewhere in the code that assumes 
>>>> that Singular is installed in $SAGE_LOCAL
>>>>
>>>> at least I got an error of this sort while trying to build Sage's docs 
>>>> in this configuration.
>>>> I'll look into it once back at the keyboard
>>>>
>>>
>>> this problem is explained in 
>>> https://trac.sagemath.org/ticket/29024#comment:8
>>>
>>> The fix needs some programming - specifically, the code in singular.pyx 
>>> calls dlopen on SINGULAR_SO,
>>> which is computed by _get_shared_lib_filename dynamically in env.py, 
>>> and assuming that it is in SAGE_LOCAL.
>>> So this probably can instead by handled using cython_aliases from the 
>>> same module (which does compute
>>> all the needed info for Singular, it seems).
>>> Or by fixing _get_shared_lib_filename so that it also searches 
>>> elsewhere.
>>>
>>>
>>>> On Fri, 11 Sep 2020, 15:10 Zachary Scherr,  wrote:
>>>>
>>>>> Hi Dima,
>>>>>
>>>>>Thanks! Downloading spkg-configure.m4 allowed me to build 
>>>>> successfully.
>>>>>
>>>>> Best,
>>>>> Zach
>>>>>
>>>>> On Friday, September 11, 2020 at 5:45:00 AM UTC-4 dim...@gmail.com 
>>>>> wrote:
>>>>>
>>>>>> On Fri, Sep 11, 2020 at 10:11 AM Dima Pasechnik  
>>>>>> wrote:
>>>>>>
>>>>>>> [sagelib-9.2.beta12] installing. Log file: 
>>>>>>> /Users/zscherr/sage/develop/logs/pkgs/sagelib-9.2.beta12.log
>>>>>>>   [sagelib-9.2.beta12] error installing, exit status 1. End of log 
>>>>>>> file:
>>>>>>>   [sagelib-9.2.beta12]   
>>>>>>> /usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 
>>>>>>> 'polys/shiftop.h' file not found
>>>>>>>   [sagelib-9.2.beta12]   #include "polys/shiftop.h"
>>>>>>>   [sagelib-9.2.beta12]^
>>>>>>>
>>>>>>> the include path looks funny with its "singular/Singular/"
>>>>>>> I don't know what brew does here, maybe it drops "singular/" bit?
>>>>>>>
>>>>>>
>>>>>> no, in fact it's all fine, it's just include flags that need to be 
>>>>>> adjusted.
>>>>>> Note that you still have 
>>>>>> -I/Users/zscherr/sage/develop/local/include/singular
>>>>>> in the failing gcc call, which seems to indicate you didn't use
>>>>>>
>>>>>> https://trac.sagemath.org/attachment/ticket/29024/spkg-configure.m4
>>>>>>
>>>>>> - of if you did, you didn't run
>>>>>>
>>>>>> make singular-clean
>>>>>>
>>>>>> ./bootstrap && ./configure
>>>>>>
>>>>>> after putting that file
>>>>>> in build/pkgs/singular/
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Try
>>>>>>
>>>>>> CXXFLAGS="$CXXFLAGS -I//usr/local/include/singular/
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Sep 10, 2020 at 9:20

[sage-devel] Re: SageMath Anaconda and Python 3.8

[Zachary Scherr]

You should probably follow the directions 
here: https://doc.sagemath.org/html/en/installation/conda.html

and install sage into its own environment so that it correctly installs all 
the dependencies.  Sage 9.2 will support python 3.8.

On Wednesday, October 7, 2020 at 2:18:27 PM UTC-4 asv...@gmail.com wrote:

> My Anaconda is instaled with Python 3.8.
> I tried to attach Sage to Anaconda by running one of the commands listed 
> here
> https://anaconda.org/conda-forge/sage
> However, there is python incompatibility. Is there any plan for an upgrade?
>
> The message on a terminal window is 
>
>
> UnsatisfiableError: The following specifications were found
> to be incompatible with the existing python installation in your 
> environment: 
>
> Specifications: 
> - sage -> 
> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0'] 
> Your python: python=3.8 
>
> If python is on the left-most side of the chain, that's the version you've 
> asked for. 
> When python appears to the right, that indicates that the thing on the 
> left is somehow 
> not available for the python version you are constrained to. Note that 
> conda will not 
> change your python version to a different minor version unless you 
> explicitly specify 
> that.
>

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Re: [sage-devel] Re: Beta 12 not building (Homebrew singular issue?)

[Zachary Scherr]

I was just curious as to what the status of this issue is, and if there was 
anything I could do to help with review.  I can build rc0 using Dima's 
suggested spkg-configure.m4 fix, but I can't build it otherwise unless I 
brew unlink singular first. 

On Friday, September 11, 2020 at 6:47:23 PM UTC-4 dim...@gmail.com wrote:

> as an experiment, I hardcoded the necessary paths for using Homebrew's 
> Singular here:
>
> https://trac.sagemath.org/attachment/ticket/29024/homebrew-singular-experiment.patch
> (the part for  src/sage/libs/singular/singular.pxd is probably not needed, 
> but anyway)
>
> running tests now.
>
> On Fri, Sep 11, 2020 at 6:15 PM Dima Pasechnik  wrote:
>
>>
>>
>> On Fri, Sep 11, 2020 at 3:32 PM Dima Pasechnik  wrote:
>>
>>> I think there is at least one place elsewhere in the code that assumes 
>>> that Singular is installed in $SAGE_LOCAL
>>>
>>> at least I got an error of this sort while trying to build Sage's docs 
>>> in this configuration.
>>> I'll look into it once back at the keyboard
>>>
>>
>> this problem is explained in 
>> https://trac.sagemath.org/ticket/29024#comment:8
>>
>> The fix needs some programming - specifically, the code in singular.pyx 
>> calls dlopen on SINGULAR_SO,
>> which is computed by _get_shared_lib_filename dynamically in env.py, and 
>> assuming that it is in SAGE_LOCAL.
>> So this probably can instead by handled using cython_aliases from the 
>> same module (which does compute
>> all the needed info for Singular, it seems).
>> Or by fixing _get_shared_lib_filename so that it also searches elsewhere.
>>
>>
>>> On Fri, 11 Sep 2020, 15:10 Zachary Scherr,  wrote:
>>>
>>>> Hi Dima,
>>>>
>>>>Thanks! Downloading spkg-configure.m4 allowed me to build 
>>>> successfully.
>>>>
>>>> Best,
>>>> Zach
>>>>
>>>> On Friday, September 11, 2020 at 5:45:00 AM UTC-4 dim...@gmail.com 
>>>> wrote:
>>>>
>>>>> On Fri, Sep 11, 2020 at 10:11 AM Dima Pasechnik  
>>>>> wrote:
>>>>>
>>>>>> [sagelib-9.2.beta12] installing. Log file: 
>>>>>> /Users/zscherr/sage/develop/logs/pkgs/sagelib-9.2.beta12.log
>>>>>>   [sagelib-9.2.beta12] error installing, exit status 1. End of log 
>>>>>> file:
>>>>>>   [sagelib-9.2.beta12]   
>>>>>> /usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 
>>>>>> 'polys/shiftop.h' file not found
>>>>>>   [sagelib-9.2.beta12]   #include "polys/shiftop.h"
>>>>>>   [sagelib-9.2.beta12]^
>>>>>>
>>>>>> the include path looks funny with its "singular/Singular/"
>>>>>> I don't know what brew does here, maybe it drops "singular/" bit?
>>>>>>
>>>>>
>>>>> no, in fact it's all fine, it's just include flags that need to be 
>>>>> adjusted.
>>>>> Note that you still have 
>>>>> -I/Users/zscherr/sage/develop/local/include/singular
>>>>> in the failing gcc call, which seems to indicate you didn't use
>>>>>
>>>>> https://trac.sagemath.org/attachment/ticket/29024/spkg-configure.m4
>>>>>
>>>>> - of if you did, you didn't run
>>>>>
>>>>> make singular-clean
>>>>>
>>>>> ./bootstrap && ./configure
>>>>>
>>>>> after putting that file
>>>>> in build/pkgs/singular/
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Try
>>>>>
>>>>> CXXFLAGS="$CXXFLAGS -I//usr/local/include/singular/
>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Sep 10, 2020 at 9:20 PM Zachary Scherr  
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Matthias,
>>>>>>>
>>>>>>>It's attached to this message.
>>>>>>>
>>>>>>> Best,
>>>>>>> Zach
>>>>>>>
>>>>>>> On Thursday, September 10, 2020 at 1:07:27 PM UTC-4 Matthias Koeppe 
>>>>>>> wrote:
>>>>>>>
>>>>>>>> On Thursday, September 10, 2020 at 9:58:02 AM UTC-7, Zachary Scherr 
>>>>>>>>

[sage-devel] Question about building fflas_ffpack

[Zachary Scherr]

In an attempt to learn a little bit about sage's build system I was playing 
around with building various packages today.  From a fresh git clone I can 
build the developer branch of my Mac with homebrew without any issues. 
 However, if I just run

make fflas_ffpack

after going through the usual steps with source .homebrew-build-env and 
./configure then it crashes pretty quickly with the message:

[fflas_ffpack-2.4.3] 
***
[fflas_ffpack-2.4.3]  ERROR: BLAS not found!
[fflas_ffpack-2.4.3]
[fflas_ffpack-2.4.3]  BLAS routines are required for this library to 
compile. Please
[fflas_ffpack-2.4.3]  make sure BLAS are installed and specify its location 
with the option
[fflas_ffpack-2.4.3]  --with-blas-libs= and if necessary 
--with-blas-cflags=
[fflas_ffpack-2.4.3]  when running configure.
[fflas_ffpack-2.4.3] 
***

I'm just curious as to why make build works to build fflas_ffpack but if I 
try to build it on its own then it fails.  I've included the log file, but 
I'm guessing there's some easy explanation. 

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Found local metadata for fflas_ffpack-2.4.3
Using cached file /Users/zscherr/sage/upstream/fflas_ffpack-2.4.3.tar.bz2
fflas_ffpack-2.4.3

Setting up build directory for fflas_ffpack-2.4.3
Finished extraction
Applying patches from ../patches...
Applying ../patches/fix-ksh-pkgconfig.patch
patching file fflas-ffpack.pc.in

Host system:
Darwin Zacharys-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 
31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64

C compiler: gcc
C compiler version:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.2)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Package 'fflas_ffpack' is currently not installed
No legacy uninstaller found for 'fflas_ffpack'; nothing to do
Package blas was not found in the pkg-config search path.
Perhaps you should add the directory containing `blas.pc'
to the PKG_CONFIG_PATH environment variable
No package 'blas' found
Package cblas was not found in the pkg-config search path.
Perhaps you should add the directory containing `cblas.pc'
to the PKG_CONFIG_PATH environment variable
No package 'cblas' found
Package blas was not found in the pkg-config search path.
Perhaps you should add the directory containing `blas.pc'
to the PKG_CONFIG_PATH environment variable
No package 'blas' found
Package cblas was not found in the pkg-config search path.
Perhaps you should add the directory containing `cblas.pc'
to the PKG_CONFIG_PATH environment variable
No package 'cblas' found
*
Using --with-blas-libs='' ''
*
Configuring fflas_ffpack-2.4.3
configure: WARNING: you should use --build, --host, --target
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking build system type... x86_64-apple-darwin19.6.0
checking host system type... x86_64-apple-darwin19.6.0
checking target system type... x86_64-apple-darwin19.6.0
checking for a BSD-compatible install... /usr/local/bin/ginstall -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/local/bin/gmkdir -p
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 whether to enable debugging options in the library... no
checking whether to enable profiling everything in the library... no
checking whether to enable warnings when compiling the library... no
---
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 g++ 

[sage-devel] Re: Error installing scipy-1.2.3

[Zachary Scherr]

If you rerun ./configure with

FC=gfortran-9 ./configure

Then it should use gfortran-9 as your Fortran compiler when making sage.

On Tuesday, September 15, 2020 at 3:49:22 PM UTC-4 Gabe Feinberg wrote:

>
> Hi~
>  I'm also trying to install from the source code, and I'm receiving an 
> error that spicy-1.2.3 failed to build. I've looked at the ticket you 
> posted, but I'm not sure if I'm interpreting it properly:
> I executed brew install gcc@9 at the command line before running make 
> again, but I'm still getting an error. Do I need to uninstall something 
> first?
>
> Thanks, my error log is attached.
>
> Gabe
> On Sunday, July 19, 2020 at 9:52:48 AM UTC-4 Matthias Koeppe wrote:
>
>> https://trac.sagemath.org/ticket/30067 has a workaround.
>>
>>
>> On Sunday, July 19, 2020 at 2:25:40 AM UTC-7, Caleb Springer wrote:
>>>
>>> I am trying to install Sage from source code on a new 2020 MacBook Air 
>>> with macOS 10.15.6.
>>>
>>> Unfortunately, scipy-1.2.3 failed to install.  I am posting this here 
>>> with the log file attached because the installer directed me to do so. 
>>>
>>> Incidentally, I can actually still call Sage from the terminal, and 
>>> basic commands work correctly. (I am actually too ignorant to know what 
>>> parts of Sage are broken by scipy-1.2.3 being absent.)
>>>
>>

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Re: [sage-devel] Re: Beta 12 not building (Homebrew singular issue?)

[Zachary Scherr]

Hi Dima,

   Thanks! Downloading spkg-configure.m4 allowed me to build successfully.

Best,
Zach

On Friday, September 11, 2020 at 5:45:00 AM UTC-4 dim...@gmail.com wrote:

> On Fri, Sep 11, 2020 at 10:11 AM Dima Pasechnik  wrote:
>
>> [sagelib-9.2.beta12] installing. Log file: 
>> /Users/zscherr/sage/develop/logs/pkgs/sagelib-9.2.beta12.log
>>   [sagelib-9.2.beta12] error installing, exit status 1. End of log file:
>>   [sagelib-9.2.beta12]   
>> /usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 
>> 'polys/shiftop.h' file not found
>>   [sagelib-9.2.beta12]   #include "polys/shiftop.h"
>>   [sagelib-9.2.beta12]^
>>
>> the include path looks funny with its "singular/Singular/"
>> I don't know what brew does here, maybe it drops "singular/" bit?
>>
>
> no, in fact it's all fine, it's just include flags that need to be 
> adjusted.
> Note that you still have 
> -I/Users/zscherr/sage/develop/local/include/singular
> in the failing gcc call, which seems to indicate you didn't use
>
> https://trac.sagemath.org/attachment/ticket/29024/spkg-configure.m4
>
> - of if you did, you didn't run
>
> make singular-clean
>
> ./bootstrap && ./configure
>
> after putting that file
> in build/pkgs/singular/
>
>
>
>
> Try
>
> CXXFLAGS="$CXXFLAGS -I//usr/local/include/singular/
>
>>
>>
>> On Thu, Sep 10, 2020 at 9:20 PM Zachary Scherr  wrote:
>>
>>> Hi Matthias,
>>>
>>>It's attached to this message.
>>>
>>> Best,
>>> Zach
>>>
>>> On Thursday, September 10, 2020 at 1:07:27 PM UTC-4 Matthias Koeppe 
>>> wrote:
>>>
>>>> On Thursday, September 10, 2020 at 9:58:02 AM UTC-7, Zachary Scherr 
>>>> wrote:
>>>>>
>>>>>
>>>>> Obviously this is not a big deal since I can just brew uninstall 
>>>>> singular and then it builds successfully, but I've been wanting to 
>>>>> contribute to sage development so I'm going to take this as an 
>>>>> opportunity 
>>>>> to try to track down what's going on. 
>>>>>
>>>>>
>>>> Yes, this is much appreciated. So far I can't reproduce the error here 
>>>> (after installing homebrew's singular), unfortunately. 
>>>>
>>>> Could you post install.log please?
>>>>
>>> -- 
>>> 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.
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>>> https://groups.google.com/d/msgid/sage-devel/3c9f01e9-ded6-43bd-8861-301d1e97a06an%40googlegroups.com
>>>  
>>> <https://groups.google.com/d/msgid/sage-devel/3c9f01e9-ded6-43bd-8861-301d1e97a06an%40googlegroups.com?utm_medium=email_source=footer>
>>> .
>>>
>>

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[sage-devel] Re: Beta 12 not building (Homebrew singular issue?)

[Zachary Scherr]

Hi Matthias,

   It's attached to this message.

Best,
Zach

On Thursday, September 10, 2020 at 1:07:27 PM UTC-4 Matthias Koeppe wrote:

> On Thursday, September 10, 2020 at 9:58:02 AM UTC-7, Zachary Scherr wrote:
>>
>>
>> Obviously this is not a big deal since I can just brew uninstall singular 
>> and then it builds successfully, but I've been wanting to contribute to 
>> sage development so I'm going to take this as an opportunity to try to 
>> track down what's going on. 
>>
>>
> Yes, this is much appreciated. So far I can't reproduce the error here 
> (after installing homebrew's singular), unfortunately. 
>
> Could you post install.log please?
>

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*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
 *)
 *)
 *v*)
 *v*)
 *v*x*)
 *v*x*)
 *x*)
 *x*)
 ;;
 ;;
 ;;
 ;;
 ;;
 ;;
 ;;
 ;;
 IFS=$_mlIFS;
 IFS=$_mlIFS;
 IFS=' ';
 IFS=' ';
 MODULES_USE_COMPAT_VERSION=1;
 _mlIFS=$IFS;
 _mlIFS=$IFS;
 _mlre="${_mlre:-}${_mlv}='`eval 'echo ${'$_mlrv':-}'`' ";
 _mlre="${_mlre:-}${_mlv}='`eval 'echo ${'$_mlrv':-}'`' ";
 _mlre="${_mlre:-}${_mlv}_modquar='`eval 'echo ${'$_mlv'}'`' ";
 _mlre="${_mlre:-}${_mlv}_modquar='`eval 'echo ${'$_mlv'}'`' ";
 _mlrv="MODULES_RUNENV_${_mlv}";
 _mlrv="MODULES_RUNENV_${_mlv}";
 _mlshdbg=''
 _mlshdbg=''
 _mlshdbg='v'
 _mlshdbg='v'
 _mlshdbg='vx'
 _mlshdbg='vx'
 _mlshdbg='x'
 _mlshdbg='x'
 _mlstatus=$?;
 _mlstatus=$?;
 case "$-" in 
 case "$-" in 
 do
 do
 done;
 done;
 echo "Cannot switch to Modules $swname version, command not found";
 echo "Switching to Modules $swname version";
 else
 else
 else
 else
 else
 else
 esac;
 esac;
 eval `/usr/bin/tclsh /usr/local/Cellar/modules/4.5.3/libexec/modulecmd.tcl 
bash "$@"`;
 eval `/usr/bin/tclsh /usr/local/Cellar/modules/4.5.3/libexec/modulecmd.tcl 
bash "$@"`;
 eval `eval ${_mlre} /usr/bin/tclsh 
/usr/local/Cellar/modules/4.5.3/libexec/modulecmd.tcl bash '"$@"'`;
 eval `eval ${_mlre} /usr/bin/tclsh 
/usr/local/Cellar/modules/4.5.3/libexec/modulecmd.tcl bash '"$@"'`;
 export MODULES_USE_COMPAT_VERSION;
 fi
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 fi;
 for _mlv in ${MODULES_RUN_QUARANTINE:-};
 for _mlv in ${MODULES_RUN_QUARANTINE:-};
 if [ "${MODULES_SILENT_SHELL_DEBUG:-0}" = '1' ]; then
 if [ "${MODULES_SILENT_SHELL_DEBUG:-0}" = '1' ]; then
 if [ "${MODULES_USE_COMPAT_VERSION:-0}" = '1' ]; then
 if [ "${_mlv}" = "${_mlv##*[!A-Za-z0-9_]}" -a "${_mlv}" = "${_mlv#[0-9]}" ]; 
then
 if [ "${_mlv}" = "${_mlv##*[!A-Za-z0-9_]}" -a "${_mlv}" = "${_mlv#[0-9]}" ]; 
then
 if [ $swfound -eq 0 ]; then
 if [ -e /usr/local/Cellar/modules/4.5.3/libexec/modulecmd-compat ]; then
 if [ -e /usr/local/Cellar/modules/4.5.3/libexec/modulecmd.tcl ]; then
 if [ -n "${IFS+x}" ]; then
 if [ -n "${IFS+x}" ]; then
 if [ -n "${_mlIFS+x}" ]; then
 if [ -n "${_mlIFS+x}" ]; then
 if [ -n "${_mlre:-}" ]; then
 if [ -n "${_mlre:-}" ]; then
 if [ -n "${_mlshdbg:-}" ]; then
 if [ -n "${_mlshdbg:-}" ]; then
 if [ -n "`eval 'echo ${'$_mlv'+x}'`" ]; then
 if [ -n "`eval 'echo ${'$_mlv'+x}'`" ]; then
 return $_mlstatus
 return $_mlstatus
 return 1;
 set +v;
 set +v;
 set +vx;
 set +vx;
 set +x;
 set +x;
 set -$_mlshdbg;
 set -$_mlshdbg;
 source /usr/local/Cellar/modules/4.5.3/init/bash;
 typeset swfound=0;
 typeset swfound=0;
 typeset swname='compatibility';
 typeset swname='main';
 unset IFS;
 unset IFS;
 unset MODULES_USE_COMPAT_VERSION;
 unset _mlre _mlIFS;
 unset _mlre _mlIFS;
 unset _mlre _mlv _mlrv _mlIFS;
 unset _mlre _mlv _mlrv _mlIFS;
 unset _mlshdbg;
 unset _mlshdbg;
ACLOCAL_PATH=/usr/local/opt/gettext/share/aclocal:/usr/local/opt/gettext/share/aclocal:
BASH_ENV=/usr/local/Cellar/modules/4.5.3/init/bash
BASH_FUNC__module_raw%%=() {  unset _mlshdbg;
BASH_FUNC_ml%%=() {  module ml "$@"
BASH_FUNC_module%%=() {  unset _mlshdbg;
BASH_FUNC_switchml%%=() {  typeset swfound=1;
BAT_PAGER=/Users/zscherr/.bat_pager.sh
COLORFGBG=7;0
COLORTERM=truecolor
CPATH=/usr/local/opt/readline/include:/usr/local/include:/usr/local/opt/readline/include:/usr/local/include
DISPLAY=/private/tmp/com.apple.launchd.UU7qR1WGkL/org.macosforge.xquartz:0
EDITOR=vim
ENV=/usr/local/Cellar/modules/4.5.3/init/profile.sh
FPATH=/usr/local/Cellar/modules/4.5.3/init/zsh-functions:/Users/zscher

[sage-devel] Re: Beta 12 not building (Homebrew singular issue?)

[Zachary Scherr]

Nope, my workflow for checking out the latest beta was just:

./bootstrap
source .homebrew-build-env
./configure
make -j8 V=0 build

Obviously this is not a big deal since I can just brew uninstall singular 
and then it builds successfully, but I've been wanting to contribute to 
sage development so I'm going to take this as an opportunity to try to 
track down what's going on. 

On Thursday, September 10, 2020 at 12:44:28 AM UTC-4 Matthias Koeppe wrote:

> You don't happen to set CFLAGS or CPPFLAGS by any chance? 
>
> The problem in the failing compile command from your log is that 
> "-I/Users/zscherr/sage/develop/local/include" appears after 
> "-I/usr/local/include". It should appear before. 
>
> gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common 
> -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot 
> /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk 
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include 
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
>  
> -I./sage/cpython -I/Users/zscherr/sage/develop/local/include/singular 
> -I/Users/zscherr/sage/develop/build/pkgs/sagelib/src 
> -I/Users/zscherr/sage/develop/build/pkgs/sagelib/src/sage/ext 
> -I/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/include/python3.8
>  
> -I/Users/zscherr/sage/develop/local/lib/python3.8/site-packages/numpy/core/include
>  
> -Ibuild/cythonized -I/usr/local/include 
> -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include 
> -I/Users/zscherr/sage/develop/local/include 
> -I/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/include/python3.8
>  
> -c 
> build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.cpp
>  
> -o 
> build/temp.macosx-10.15-x86_64-3.8/build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.o
>  
> -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -DSING_NDEBUG 
> -DOM_NDEBUG -I/Users/zscherr/sage/develop/local/include/singular -std=c++11
>
> On Wednesday, September 9, 2020 at 8:52:07 PM UTC-7, Zachary Scherr wrote:
>>
>>Running ./sage -sh -c 'pkg-config --cflags singular' with home-brew's 
>> singular installed gives:
>>
>> -DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG 
>> -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG 
>> -I/Users/zscherr/sage/develop/local/include/singular
>>
>> my env is a mess, but I do source .homebrew-build-env, here is what I 
>> think are the relevant variables:
>>
>>
>> PATH=/usr/local/opt/gettext/bin:/Users/zscherr/perl5/bin:/usr/local/sbin:/usr/local/Cellar/modules/4.5.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin
>>
>> PKG_CONFIG_PATH=/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:
>>
>> LIBRARY_PATH=/usr/local/opt/gcc@9/lib/gcc/9:/usr/local/opt/readline/lib:/usr/local/lib
>> CPATH=/usr/local/opt/readline/include:/usr/local/include
>> ACLOCAL_PATH=/usr/local/opt/gettext/share/aclocal:
>>
>> As expected, if I brew uninstall singular then running ./sage -sh -c 
>> 'pkg-config --cflags singular' gives
>>
>> -DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG 
>> -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG 
>> -I/Users/zscherr/sage/develop/local/include/singular
>>
>> I was able to build beta 11 so I can try to git bisect if you think that 
>> would be useful.
>>
>>
>>
>>
>> On Wednesday, September 9, 2020 at 11:04:16 PM UTC-4 Matthias Koeppe 
>> wrote:
>>
>>> On Wednesday, September 9, 2020 at 7:57:18 PM UTC-7, Matthias Koeppe 
>>> wrote:
>>>>
>>>> On Wednesday, September 9, 2020 at 6:49:36 PM UTC-7, Zachary Scherr 
>>>> wrote:
>>>>>
>>>>>I tried to build the most recent beta version of sage and it would 
>>>>> appear that it's taking issue with the fact that I have singular 
>>>>> installed 
>>>>> on my Mac 10.15.6 through homebrew.  Homebrew's version is singular 
>>>>> 4.1.3p2 
>>>>> and when I try to build sage I get errors like:
>>>>>
>>>>> "In file included from 
>>>>> build/cythonized/sage/rings/polynomial/plural.cpp:684:
>>>>> /usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 
>>>>> 'polys/shiftop.h' file not f

[sage-devel] Re: Beta 12 not building (Homebrew singular issue?)

[Zachary Scherr]

Hi Matthias,

   Running ./sage -sh -c 'pkg-config --cflags singular' with home-brew's 
singular installed gives:

-DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG 
-DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG 
-I/Users/zscherr/sage/develop/local/include/singular

my env is a mess, but I do source .homebrew-build-env, here is what I think 
are the relevant variables:

PATH=/usr/local/opt/gettext/bin:/Users/zscherr/perl5/bin:/usr/local/sbin:/usr/local/Cellar/modules/4.5.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin
PKG_CONFIG_PATH=/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:
LIBRARY_PATH=/usr/local/opt/gcc@9/lib/gcc/9:/usr/local/opt/readline/lib:/usr/local/lib
CPATH=/usr/local/opt/readline/include:/usr/local/include
ACLOCAL_PATH=/usr/local/opt/gettext/share/aclocal:

As expected, if I brew uninstall singular then running ./sage -sh -c 
'pkg-config --cflags singular' gives

-DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG -DSING_NDEBUG 
-DOM_NDEBUG -DSING_NDEBUG -DOM_NDEBUG 
-I/Users/zscherr/sage/develop/local/include/singular

I was able to build beta 11 so I can try to git bisect if you think that 
would be useful.




On Wednesday, September 9, 2020 at 11:04:16 PM UTC-4 Matthias Koeppe wrote:

> On Wednesday, September 9, 2020 at 7:57:18 PM UTC-7, Matthias Koeppe wrote:
>>
>> On Wednesday, September 9, 2020 at 6:49:36 PM UTC-7, Zachary Scherr wrote:
>>>
>>>I tried to build the most recent beta version of sage and it would 
>>> appear that it's taking issue with the fact that I have singular installed 
>>> on my Mac 10.15.6 through homebrew.  Homebrew's version is singular 4.1.3p2 
>>> and when I try to build sage I get errors like:
>>>
>>> "In file included from 
>>> build/cythonized/sage/rings/polynomial/plural.cpp:684:
>>> /usr/local/include/singular/Singular/libsingular.h:15:10: fatal error: 
>>> 'polys/shiftop.h' file not found
>>> #include "polys/shiftop.h"
>>>
>>>
>> Could you run the following please:
>> ./sage -sh -c 'pkg-config --cflags singular'
>>
>>
> Also could you post the output of "env"? 
> (Do you use .homebrew-build-env to set environment variables?)
>
>

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Re: [sage-devel] trouble compiling development version

[Zachary Scherr]

Also, it says that you have homebrew on your system.  Does 'brew doctor' 
complain about having python on your path? Maybe you might want to try to 
delete all of the old versions of python on your system and remove them 
from your PATH.

You might also consider following the homebrew recommendations (installing 
gcc@9 will stop gfortran 9 from compiling from scratch) and then running 
"source /Applications/sage/.homebrew-build-env" before you configure and 
make.

On Tuesday, September 1, 2020 at 6:49:12 PM UTC-4 Zachary Scherr wrote:

> You said that you are running 10.15.6 but something looks very bizarre 
> with the python3 that configure is picking up.  It looks like it is using
>
> /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
>
> since this python is first in your PATH.
>
> Could you try running this python and then issuing:
>
> >>> import sysconfig
> >>> sysconfig.get_config_var('MACOSX_DEPLOYMENT_TARGET')
>
> If you see it saying '10.9' then this might be related to your problem.
>
> On my Catalina, configure finds python3 in /usr/bin, and if I issue those 
> same commands I get '10.14'.  So maybe your PATH is causing sage to find an 
> older version of python 3 which is causing things to mess up.  Maybe 
> somebody with more experience can chime in, but I would guess that this is 
> related to your problem.
>
> On Tuesday, September 1, 2020 at 6:36:28 PM UTC-4 dim...@gmail.com wrote:
>
>> On Tue, Sep 1, 2020 at 6:13 PM Anne Schilling  
>> wrote: 
>> > 
>> > Hi! 
>> > 
>> > I am having trouble (once again) to compile the latest development 
>> version of sage, see 
>> > 
>> > https://www.math.ucdavis.edu/~anne/kiwisolver-1.0.1.log 
>> > 
>> > This is on MacOS 10.15.6. 
>> > 
>> > Any ideas? 
>> see 
>> https://kiwisolver.readthedocs.io/en/latest/basis/installation.html 
>> it says 
>> --- 
>> For MacOSX users on OSX Mojave, one needs to set 
>> MACOSX_DEPLOYMENT_TARGET to higher than 10.9 to force the compiler to 
>> use the new C++ stdlib: 
>>
>> $ export MACOSX_DEPLOYMENT_TARGET=10.10 
>> --- 
>>
>> I'd do this export and hit "make" again 
>>
>> HTH 
>> Dima 
>>
>>
>>
>> > 
>> > Anne 
>> > 
>> >  
>> > [maxima-5.44.0] Copying package files from temporary location 
>> /Applications/sage/local/var/tmp/sage/build/maxima-5.44.0/inst to 
>> /Applications/sage/local 
>> > [maxima-5.44.0] Successfully installed maxima-5.44.0 
>> > [maxima-5.44.0] Deleting temporary build directory 
>> > [maxima-5.44.0] 
>> /Applications/sage/local/var/tmp/sage/build/maxima-5.44.0 
>> > [maxima-5.44.0] Finished installing maxima-5.44.0 
>> > [gfortran-9.2.0] Finished installing gfortran-9.2.0 
>> > make[2]: *** [all-start] Error 2 
>> > 
>> > real 202m12.303s 
>> > user 144m55.131s 
>> > sys 25m56.364s 
>> > *** 
>> > Error building Sage. 
>> > 
>> > The following package(s) may have failed to build (not necessarily 
>> > during this run of 'make all-start'): 
>> > 
>> > * package: kiwisolver-1.0.1 
>> > last build time: Sep 1 02:41 
>> > log file: /Applications/sage/logs/pkgs/kiwisolver-1.0.1.log 
>> > build directory: 
>> /Applications/sage/local/var/tmp/sage/build/kiwisolver-1.0.1 
>> > 
>> > It is safe to delete any log files and build directories, but they 
>> > contain information that is helpful for debugging build problems. 
>> > WARNING: If you now run 'make' again, the build directory of the 
>> > same version of the package will, by default, be deleted. Set the 
>> > environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this. 
>> > 
>> > make[1]: *** [all-start] Error 1 
>> > make: *** [all] Error 2 
>> > 
>> > -- 
>> > 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/0505a395-a133-47b1-956d-0334e07f9cedo%40googlegroups.com.
>>  
>>
>>
>

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Re: [sage-devel] trouble compiling development version

[Zachary Scherr]

You said that you are running 10.15.6 but something looks very bizarre with 
the python3 that configure is picking up.  It looks like it is using

/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7

since this python is first in your PATH.

Could you try running this python and then issuing:

>>> import sysconfig
>>> sysconfig.get_config_var('MACOSX_DEPLOYMENT_TARGET')

If you see it saying '10.9' then this might be related to your problem.

On my Catalina, configure finds python3 in /usr/bin, and if I issue those 
same commands I get '10.14'.  So maybe your PATH is causing sage to find an 
older version of python 3 which is causing things to mess up.  Maybe 
somebody with more experience can chime in, but I would guess that this is 
related to your problem.

On Tuesday, September 1, 2020 at 6:36:28 PM UTC-4 dim...@gmail.com wrote:

> On Tue, Sep 1, 2020 at 6:13 PM Anne Schilling  
> wrote:
> >
> > Hi!
> >
> > I am having trouble (once again) to compile the latest development 
> version of sage, see
> >
> > https://www.math.ucdavis.edu/~anne/kiwisolver-1.0.1.log
> >
> > This is on MacOS 10.15.6.
> >
> > Any ideas?
> see
> https://kiwisolver.readthedocs.io/en/latest/basis/installation.html
> it says
> ---
> For MacOSX users on OSX Mojave, one needs to set
> MACOSX_DEPLOYMENT_TARGET to higher than 10.9 to force the compiler to
> use the new C++ stdlib:
>
> $ export MACOSX_DEPLOYMENT_TARGET=10.10
> ---
>
> I'd do this export and hit "make" again
>
> HTH
> Dima
>
>
>
> >
> > Anne
> >
> > 
> > [maxima-5.44.0] Copying package files from temporary location 
> /Applications/sage/local/var/tmp/sage/build/maxima-5.44.0/inst to 
> /Applications/sage/local
> > [maxima-5.44.0] Successfully installed maxima-5.44.0
> > [maxima-5.44.0] Deleting temporary build directory
> > [maxima-5.44.0] /Applications/sage/local/var/tmp/sage/build/maxima-5.44.0
> > [maxima-5.44.0] Finished installing maxima-5.44.0
> > [gfortran-9.2.0] Finished installing gfortran-9.2.0
> > make[2]: *** [all-start] Error 2
> >
> > real 202m12.303s
> > user 144m55.131s
> > sys 25m56.364s
> > ***
> > Error building Sage.
> >
> > The following package(s) may have failed to build (not necessarily
> > during this run of 'make all-start'):
> >
> > * package: kiwisolver-1.0.1
> > last build time: Sep 1 02:41
> > log file: /Applications/sage/logs/pkgs/kiwisolver-1.0.1.log
> > build directory: 
> /Applications/sage/local/var/tmp/sage/build/kiwisolver-1.0.1
> >
> > It is safe to delete any log files and build directories, but they
> > contain information that is helpful for debugging build problems.
> > WARNING: If you now run 'make' again, the build directory of the
> > same version of the package will, by default, be deleted. Set the
> > environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
> >
> > make[1]: *** [all-start] Error 1
> > make: *** [all] Error 2
> >
> > --
> > 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/0505a395-a133-47b1-956d-0334e07f9cedo%40googlegroups.com
> .
>

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Re: [sage-devel] Cplex installation (for beginners)

[Zachary Scherr]

I think you need to run:

sage -i openssl
sage -f python3

and then you should be able to add packages through pip. 

On Wednesday, August 26, 2020 at 12:23:20 PM UTC-4 dim...@gmail.com wrote:

> On Wed, Aug 26, 2020 at 5:10 PM David Coudert  wrote:
> >
> > Hello,
> >
> > I'm posting this here as it may help improving the documentation of sage 
> math and the install guide of Cplex.
> >
> > A colleague (with very little system knowledge) just installed sagemath 
> on his new macOS laptop using the precompiled binary 
> sage-9.1-OSX_10.15.4-x86_64.app.dmg.
> > He also installed Cplex Studio 12.10.
> > Then he followed the install guide of Cplex from 
> https://github.com/mkoeppe/sage-numerical-backends-cplex and got the 
> following error.
> > I don't know how to solve this issue.
> >
> > Any help is more than welcome :))
> >
> > Best,
> > David.
> >
> > =
> > aioli:~ nnisse$ sage -python -m pip install sage-numerical-backends-cplex
> > pip is configured with locations that require TLS/SSL, however the ssl 
> module in Python is not available.
>
> 
>
> this is the 1st problem to fix, by doing
> "sage -i openssl pyopenssl"
> and crossing your fingers...
>
>
>
>
> > Collecting sage-numerical-backends-cplex
> > Retrying (Retry(total=4, connect=None, read=None, redirect=None, 
> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
> URL because the SSL module is not available.")': 
> /simple/sage-numerical-backends-cplex/
> > Retrying (Retry(total=3, connect=None, read=None, redirect=None, 
> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
> URL because the SSL module is not available.")': 
> /simple/sage-numerical-backends-cplex/
> > Retrying (Retry(total=2, connect=None, read=None, redirect=None, 
> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
> URL because the SSL module is not available.")': 
> /simple/sage-numerical-backends-cplex/
> > Retrying (Retry(total=1, connect=None, read=None, redirect=None, 
> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
> URL because the SSL module is not available.")': 
> /simple/sage-numerical-backends-cplex/
> > Retrying (Retry(total=0, connect=None, read=None, redirect=None, 
> status=None)) after connection broken by 'SSLError("Can't connect to HTTPS 
> URL because the SSL module is not available.")': 
> /simple/sage-numerical-backends-cplex/
> > Could not fetch URL 
> https://pypi.org/simple/sage-numerical-backends-cplex/: There was a 
> problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', 
> port=443): Max retries exceeded with url: 
> /simple/sage-numerical-backends-cplex/ (Caused by SSLError("Can't connect 
> to HTTPS URL because the SSL module is not available.")) - skipping
> > Could not find a version that satisfies the requirement 
> sage-numerical-backends-cplex (from versions: )
> > No matching distribution found for sage-numerical-backends-cplex
> > pip is configured with locations that require TLS/SSL, however the ssl 
> module in Python is not available.
> > Could not fetch URL https://pypi.org/simple/pip/: There was a problem 
> confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', 
> port=443): Max retries exceeded with url: /simple/pip/ (Caused by 
> SSLError("Can't connect to HTTPS URL because the SSL module is not 
> available.")) - skipping
> > =
> >
> > --
> > 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/45eb9955-098f-4583-9716-b1651ce89845n%40googlegroups.com
> .
>

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Re: [sage-devel] make doc gets stuck at thematic_tutorials

[Zachary Scherr]

Ah, thanks.  

On Monday, August 17, 2020 at 8:30:23 PM UTC-4 François Bissey wrote:

> You are probably experiencing https://trac.sagemath.org/ticket/30351
>
> > On 18/08/2020, at 12:28 PM, Zachary Scherr  wrote:
> > 
> > I tried to build the documentation on 9.2 beta 8 and the documentation 
> building seems to get hang on:
> > 
> > [dochtml]
> > [dochtml] [thematic_] building [html]: targets for 83 source files that 
> are out of date
> > [dochtml] [thematic_] updating environment: [new config] 83 added, 0 
> changed, 0 removed
> > 
> > When I hit ctrl+C I got:
> > 
> > ^C[dochtml] Error building the documentation.
> > [dochtml] Traceback (most recent call last):
> > [dochtml] File 
> "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py",
>  
> line 193, in _run_module_as_main
> > [dochtml] "__main__", mod_spec)
> > [dochtml] File 
> "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py",
>  
> line 85, in _run_code
> > [dochtml] exec(code, run_globals)
> > [dochtml] File 
> "/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py",
>  
> line 2, in 
> > [dochtml] main()
> > [dochtml] File 
> "/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
>  
> line 1721, in main
> > [dochtml] builder()
> > [dochtml] File 
> "/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
>  
> line 337, in _wrapper
> > [dochtml] build_many(build_other_doc, L)
> > [dochtml] File 
> "/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
>  
> line 281, in build_many
> > [dochtml] _build_many(target, args, processes=NUM_THREADS)
> > [dochtml] File 
> "/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py",
>  
> line 263, in build_many
> > [dochtml] waited_pid, waited_exitcode = wait_for_one()
> > [dochtml] File 
> "/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py",
>  
> line 179, in wait_for_one
> > [dochtml] pid, sts = os.wait()
> > [dochtml] File "src/cysignals/signals.pyx", line 320, in 
> cysignals.signals.python_check_interrupt
> > [dochtml] KeyboardInterrupt
> > 
> > any ideas?
> > 
> > 
> > 
> > -- 
> > 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/542ad0c5-acd5-4cd5-aa8b-66cc711c9facn%40googlegroups.com
> .
>
>

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[sage-devel] make doc gets stuck at thematic_tutorials

[Zachary Scherr]

I tried to build the documentation on 9.2 beta 8 and the documentation 
building seems to get hang on:

[dochtml]
[dochtml] [thematic_] building [html]: targets for 83 source files that are 
out of date
[dochtml] [thematic_] updating environment: [new config] 83 added, 0 
changed, 0 removed

When I hit ctrl+C I got:

^C[dochtml] Error building the documentation.
[dochtml] Traceback (most recent call last):
[dochtml]   File 
"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py",
 
line 193, in _run_module_as_main
[dochtml] "__main__", mod_spec)
[dochtml]   File 
"/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.7/lib/python3.7/runpy.py",
 
line 85, in _run_code
[dochtml] exec(code, run_globals)
[dochtml]   File 
"/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py",
 
line 2, in 
[dochtml] main()
[dochtml]   File 
"/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
 
line 1721, in main
[dochtml] builder()
[dochtml]   File 
"/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
 
line 337, in _wrapper
[dochtml] build_many(build_other_doc, L)
[dochtml]   File 
"/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py",
 
line 281, in build_many
[dochtml] _build_many(target, args, processes=NUM_THREADS)
[dochtml]   File 
"/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py",
 
line 263, in build_many
[dochtml] waited_pid, waited_exitcode = wait_for_one()
[dochtml]   File 
"/Users/zscherr/sage/develop/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py",
 
line 179, in wait_for_one
[dochtml] pid, sts = os.wait()
[dochtml]   File "src/cysignals/signals.pyx", line 320, in 
cysignals.signals.python_check_interrupt
[dochtml] KeyboardInterrupt

any ideas?


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Re: [sage-devel] unable to locate pari.cfg

[Zachary Scherr]

In an attempt to be helpful I tried to recreate the error with fewer 
options to configure.  It appears that on Catalina the error is caused by:

./configure --with-system-gp2c=no

On Sunday, July 26, 2020 at 6:00:45 PM UTC-4 Samuel Lelievre wrote:

> 2020-07-25 21:30:25 UTC Samuel Lelièvre:
>
> >
> > 2020-05-25 20:25:58 UTC, Dima Pasechnik: 
> > > 
> > > try adding 
> > > 
> > > --with-system-pari=no 
> > > 
> > > although indeed this looks like a bug to me 
> >
> > Thanks! In fact `--with-system-pari=no` is already there. 
> > (The flags are in the order found in `./configure --help`.) 
>
> Should I open a ticket? If so what should I call it?
>

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[sage-devel] Re: Problem building develop branch

[Zachary Scherr]

A brief look at the log file suggests that it's using python 2 from 
homebrew.  Maybe try remove python@2 from homebrew? I don't think they 
support it anymore.

On Sunday, July 19, 2020 at 2:55:04 PM UTC-4 dwb...@gmail.com wrote:

> I am trying to build on an iMac running MacOS 10.14.6 (Mojave). I have 
> homebrew installed.
>
> I can build the master branch.
>
> When I try to build the develop branch, I quickly run into this:
>
> [patch-2.7.5] ValueError: unsupported hash type sha512
>
> [patch-2.7.5] 
> 
>
> [patch-2.7.5] Traceback (most recent call last):
>
> [patch-2.7.5]   File 
> "/Users/bump/sagemath/sage/build/bin/../sage_bootstrap/download/cmdline.py", 
> line 130, in run_safe
>
> [patch-2.7.5] run()
>
> [patch-2.7.5]   File 
> "/Users/bump/sagemath/sage/build/bin/../sage_bootstrap/download/cmdline.py", 
> line 112, in run
>
> [patch-2.7.5] app.download_tarball(args.url_or_tarball, 
> args.destination, args.allow_upstream)
>
> [patch-2.7.5]   File 
> "/Users/bump/sagemath/sage/build/bin/../sage_bootstrap/download/app.py", 
> line 41, in download_tarball
>
> [patch-2.7.5] tarball.download(allow_upstream=allow_upstream)
>
> [patch-2.7.5]   File 
> "/Users/bump/sagemath/sage/build/bin/../sage_bootstrap/tarball.py", line 
> 145, in download
>
> [patch-2.7.5] if self.checksum_verifies():
>
> [patch-2.7.5]   File 
> "/Users/bump/sagemath/sage/build/bin/../sage_bootstrap/tarball.py", line 
> 132, in checksum_verifies
>
> [patch-2.7.5] sha1 = self._compute_sha1()
>
> [patch-2.7.5]   File 
> "/Users/bump/sagemath/sage/build/bin/../sage_bootstrap/tarball.py", line 
> 118, in _compute_sha1
>
> [patch-2.7.5] return self._compute_hash(hashlib.sha1())
>
> [patch-2.7.5] AttributeError: 'module' object has no attribute 'sha1'
>
> [patch-2.7.5] 
> 
>
> [patch-2.7.5] 
> 
>
> [patch-2.7.5] Error downloading patch-2.7.5.tar.gz
>
> [patch-2.7.5] 
> 
>
>
>
> I'm attaching patch-2.7.5.log.
>
>
> Daniel Bump
>
>
>
>
>

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[sage-devel] Re: problem building ecl on osx

[Zachary Scherr]

I don't think homebrew recommends you linking it since Mac ships with 
makeinfo and install-info, but putting it on the path to build sage seems 
fair.

On Sunday, July 19, 2020 at 10:15:35 AM UTC-4 dei...@gmail.com wrote:

> Thanks, this worked (it was already installed, but not linked).
>
>
> On Saturday, July 18, 2020 at 11:59:03 PM UTC-4, Zachary Scherr wrote:
>>
>> I think it might be related to Mac having an old version of makeinfo.  I 
>> see from your config.log that you use homebrew.  To get ECL to build you 
>> can try
>>
>> brew install texinfo
>> export PATH="/usr/local/opt/texinfo/bin:$PATH"
>>
>> and then rerunning configure and make.  I haven't tested with sage, but I 
>> downloaded ECL and that allowed me to build it (it wouldn't build using 
>> Mac's default makeinfo).  It's maybe worth including that in the list of 
>> optional homebrew packages and then updated .homebrew-build-env
>> On Saturday, July 18, 2020 at 10:08:58 PM UTC-4 Matthias Koeppe wrote:
>>
>>> I have opened https://trac.sagemath.org/ticket/30173 for this
>>>
>>>
>>> On Saturday, July 18, 2020 at 5:50:30 PM UTC-7, David Einstein wrote:
>>>>
>>>> Attempting to rebuild sage I run into problems building ecl.  This 
>>>> baffles me, as it seems to die while building the documentation for ecl.
>>>> Attached are the config.log and ecl-20.4.24.p0.log
>>>>
>>>

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[sage-devel] Re: problem building ecl on osx

[Zachary Scherr]

I think it might be related to Mac having an old version of makeinfo.  I 
see from your config.log that you use homebrew.  To get ECL to build you 
can try

brew install texinfo
export PATH="/usr/local/opt/texinfo/bin:$PATH"

and then rerunning configure and make.  I haven't tested with sage, but I 
downloaded ECL and that allowed me to build it (it wouldn't build using 
Mac's default makeinfo).  It's maybe worth including that in the list of 
optional homebrew packages and then updated .homebrew-build-env
On Saturday, July 18, 2020 at 10:08:58 PM UTC-4 Matthias Koeppe wrote:

> I have opened https://trac.sagemath.org/ticket/30173 for this
>
>
> On Saturday, July 18, 2020 at 5:50:30 PM UTC-7, David Einstein wrote:
>>
>> Attempting to rebuild sage I run into problems building ecl.  This 
>> baffles me, as it seems to die while building the documentation for ecl.
>> Attached are the config.log and ecl-20.4.24.p0.log
>>
>

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[sage-devel] Re: cryptominisat does not buld on Ubuntu 20.04

[Zachary Scherr]

I was able to successfully build cryptominisat using an Ubuntu 20.04 docker 
image.  Some weird things I noticed from your log files:

config log says you have boost lib >= 1.66 yet your cryptominisat log file 
says "Boost 1.46 found".  On the next line it says:

"-- Found Boost components: program_options"

which seems to be related to all of the errors.

I'll let a more experienced person chime in, but I imagine that if you get 
the latest version of libboost-dev and cmake from apt and let sage find it 
via ./configure then maybe cyrptominisat will build.

On Monday, July 13, 2020 at 11:26:06 PM UTC-4 Andrey Novoseltsev wrote:

> On Monday, 13 July 2020 21:11:11 UTC-6, Matthias Koeppe wrote:
>>
>> Please also send the top-level config.log 
>>
>
> Attached!
>
>
>> Lots of optional and experimental packages are broken. See 
>> https://trac.sagemath.org/ticket/29900 - which needs help.
>>
>
> Thank you for working on this! Can't commit to more help than supplying 
> logs...
>
>

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Re: [sage-devel] Unable to build sage

[Zachary Scherr]

Seems to be related to https://github.com/scipy/scipy/issues/11611 and as 
was pointed out above was fixed in version 1.5.

I'd like to propose two workarounds for people who can no longer build sage 
and stumble into this thread (either should allow scipy 1.2.3 to build)

1). Use fortran 9:

brew install gcc@9
FC=gfortran-9 ./configure
make

2). Add a flag to fortran 10 (should work if you have gcc 10 regardless of 
whether you have homebrew or not):

./configure
FFLAGS=-fallow-argument-mismatch make

On Saturday, July 4, 2020 at 7:48:43 PM UTC-4 hel...@potuz.net wrote:

> On Jul 04, Dima Pasechnik wrote:
> >I guess this is due to gfortran 10.
> >We still do not support gcc 10, I think.
> >Can you downgrade it to gfortran 9?
> >
> For what its worth, here running arch, 
>
> 1) removing line 153 from build/pkgs/gcc/spkg-configure.m4
> 2) adding a newer scipy: upstream/scipy-1.5.0.tar.gz
> 3) pulling pybind11 from this commit 
>
> https://git.sagemath.org/sage.git/commit/?id=fa20111935c171f1d99c410110967350f4facea2
>
> allowed me to upgrade without a glitch so far
>
> R. 
> >
> >On Sat, 4 Jul 2020, 23:06 Daniel Bump, <[1]dwb...@gmail.com> wrote:
> >
> >
> >
> > On Saturday, July 4, 2020 at 2:52:06 PM UTC-7, Dima Pasechnik wrote:
> >
> > Please post top config.log and also the full logs/pkgs/scipy-...log
> >
> >
> > Attached.
> >
> > Thanks,
> > Dan 
> >
> > --
> > You received this message because you are subscribed to the Google Groups
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> > email to [2]sage-devel+...@googlegroups.com.
> > To view this discussion on the web visit [3]https://groups.google.com/d/
> > msgid/sage-devel/117843bf-3793-47fb-a952-9e58ad31da9co%
> 40googlegroups.com.
> >
> >--
> >You received this message because you are subscribed to the Google Groups
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> email
> >to [4]sage-devel+...@googlegroups.com.
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> https://groups.google.com/d/msgid/
> >sage-devel/
> >CAAWYfq0cbnv0%3DpMchh2pPmnR%2BxaC_vVjB_Ve9NOmoJUtiLtEkQ%40mail.gmail.com.
> >
> >References:
> >
> >[1] mailto:dwb...@gmail.com
> >[2] mailto:sage-devel+...@googlegroups.com
> >[3] 
> https://groups.google.com/d/msgid/sage-devel/117843bf-3793-47fb-a952-9e58ad31da9co%40googlegroups.com?utm_medium=email_source=footer
> >[4] mailto:sage-devel+...@googlegroups.com
> >[5] 
> https://groups.google.com/d/msgid/sage-devel/CAAWYfq0cbnv0%3DpMchh2pPmnR%2BxaC_vVjB_Ve9NOmoJUtiLtEkQ%40mail.gmail.com?utm_medium=email_source=footer
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Re: [sage-devel] trouble building sage on mac

[Zachary Scherr]

Also, you might also consider doing something like the following:

> cd /usr
> find -L . -name 'ftheader.h'

you should see the following locations:

./local/include/freetype2/freetype/config/ftheader.h
./local/var/homebrew/linked/freetype/include/freetype2/freetype/config/ftheader.h
./local/opt/freetype2/include/freetype2/freetype/config/ftheader.h
./local/opt/freetype/include/freetype2/freetype/config/ftheader.h
./local/Cellar/freetype/2.10.2/include/freetype2/freetype/config/ftheader.h

notice though that 
"/usr/local/Cellar/freetype/2.10.2/include/freetype2/freetype/config/ftheader.h"
 
is the real file and the others should all be symlinks of this one.

On Wednesday, July 1, 2020 at 8:26:58 AM UTC-4 Zachary Scherr wrote:

> Hi All,
>
>I just thought I would chime in on the homebrew side of things.  I have 
> freetype installed via homebrew on Catalina 10.15.5 and when I execute
>
> > pkg-config --modversion freetype2
>
> I get back 23.2.17.  Anne seemed to get back version 9.8.3, which means 
> that something is screwy with your freetype.
>
> Some things you could try:
>
> 1). If you have already installed freetype via homebrew then you can try
>  brew unlink freetype && brew link freetype
>
> 2). It's possible that "brew doctor" will pick up on the inconsistencies 
> and will give recommendations as to how to fix it.
>
> Your log file specifically mentioned that the system could not find 
> ftconfig.h.  With freetype correctly installed via homebrew you can do the 
> following:
>
> cd /usr/local/include
> ls -l | grep freetype2
>
> and you should see that that folder is symlinked to 
> /usr/local/Cellar/freetype/2.10.2/include/freetype2 which is the folder 
> that actually contains all the freetype header files.
>
> Not sure how much you want to invest in fixing this, but my suggestion 
> would be to head to /usr/local and try to find ftheader.h, which is the 
> header file that defines where ftconfig.h is located.  If you find any 
> ftheader.h file that is not originating from 
> local/Cellar/freetype/2.10.2/include/freetype2/freetype/config/ftheader.h 
> then you should delete it.
>
>
>
> On Wednesday, July 1, 2020 at 2:53:05 AM UTC-4 dim...@gmail.com wrote:
>
>>
>>
>> On Wed, 1 Jul 2020, 07:41 Anne Schilling,  wrote:
>>
>>>
>>>
>>> On Tuesday, June 30, 2020 at 12:22:47 AM UTC-7, Dima Pasechnik wrote:
>>>>
>>>>
>>>>
>>>> On Tue, 30 Jun 2020, 07:46 Anne Schilling,  
>>>> wrote:
>>>>
>>>>> Here is the new config.log file. It still does not build:
>>>>>
>>>>> https://www.math.ucdavis.edu/~anne/config.log 
>>>>> <https://www.google.com/url?q=https%3A%2F%2Fwww.math.ucdavis.edu%2F~anne%2Fconfig.log=D=1=AFQjCNGHbWAuGZkjNWZ_oCVmDNSsBSqS0w>
>>>>>
>>>>
>>>> do you get the same error while building pillow (missing header)? If 
>>>> so, it looks as if you removed the old freetype dylib files, but left 
>>>> headers there.
>>>>
>>>
>>> Thank you, but what exactly am I supposed to delete? I delete the folder 
>>> /usr/local/Cellar/freetype
>>>
>>
>> you had to delete the installation of freetype in /usr/local/{lib, 
>> include, lib/pkgconfig}. 
>>
>> and after that, (re)install freetype in Homebrew.
>>
>> Deleting /usr/local/Cellar/freetype 
>> probably was not a good idea - that is where, I guess, you have a good 
>> installation of freetype (which you should uninstall using the brew 
>> commands, not just deleting from shell)
>>
>> But I don't know whether your Homebrew is not too old. Can you do
>>
>> brew install freetype 
>>
>> (or is it freetype2) 
>>
>> paying attention to the version it mentions?
>>
>>
>> in any case, 
>>
>> ./configure --with-freetype=system 
>>
>> should force sage to build freetype on its own.
>>
>>
>>
>>> Also, did you source .homebrew-build-env
>>>> before doing ./configure && make ?
>>>> As you use libraries from Homebrew, this might be crucial.
>>>>
>>>
>>> I did that and it still does not work. See
>>>
>>> https://www.math.ucdavis.edu/~anne/config.log 
>>> <https://www.google.com/url?q=https%3A%2F%2Fwww.math.ucdavis.edu%2F~anne%2Fconfig.log=D=1=AFQjCNGHbWAuGZkjNWZ_oCVmDNSsBSqS0w>
>>>
>>> Is it possible that this might be an issue
>>>
>>> https://github.com/Homebrew/legacy-homebrew/issues/43471
>>>
>>>

Re: [sage-devel] trouble building sage on mac

[Zachary Scherr]

Hi All,

   I just thought I would chime in on the homebrew side of things.  I have 
freetype installed via homebrew on Catalina 10.15.5 and when I execute

> pkg-config --modversion freetype2

I get back 23.2.17.  Anne seemed to get back version 9.8.3, which means 
that something is screwy with your freetype.

Some things you could try:

1). If you have already installed freetype via homebrew then you can try
 brew unlink freetype && brew link freetype

2). It's possible that "brew doctor" will pick up on the inconsistencies 
and will give recommendations as to how to fix it.

Your log file specifically mentioned that the system could not find 
ftconfig.h.  With freetype correctly installed via homebrew you can do the 
following:

cd /usr/local/include
ls -l | grep freetype2

and you should see that that folder is symlinked to 
/usr/local/Cellar/freetype/2.10.2/include/freetype2 which is the folder 
that actually contains all the freetype header files.

Not sure how much you want to invest in fixing this, but my suggestion 
would be to head to /usr/local and try to find ftheader.h, which is the 
header file that defines where ftconfig.h is located.  If you find any 
ftheader.h file that is not originating from 
local/Cellar/freetype/2.10.2/include/freetype2/freetype/config/ftheader.h 
then you should delete it.



On Wednesday, July 1, 2020 at 2:53:05 AM UTC-4 dim...@gmail.com wrote:

>
>
> On Wed, 1 Jul 2020, 07:41 Anne Schilling,  wrote:
>
>>
>>
>> On Tuesday, June 30, 2020 at 12:22:47 AM UTC-7, Dima Pasechnik wrote:
>>>
>>>
>>>
>>> On Tue, 30 Jun 2020, 07:46 Anne Schilling,  wrote:
>>>
 Here is the new config.log file. It still does not build:

 https://www.math.ucdavis.edu/~anne/config.log 
 

>>>
>>> do you get the same error while building pillow (missing header)? If so, 
>>> it looks as if you removed the old freetype dylib files, but left headers 
>>> there.
>>>
>>
>> Thank you, but what exactly am I supposed to delete? I delete the folder 
>> /usr/local/Cellar/freetype
>>
>
> you had to delete the installation of freetype in /usr/local/{lib, 
> include, lib/pkgconfig}. 
>
> and after that, (re)install freetype in Homebrew.
>
> Deleting /usr/local/Cellar/freetype 
> probably was not a good idea - that is where, I guess, you have a good 
> installation of freetype (which you should uninstall using the brew 
> commands, not just deleting from shell)
>
> But I don't know whether your Homebrew is not too old. Can you do
>
> brew install freetype 
>
> (or is it freetype2) 
>
> paying attention to the version it mentions?
>
>
> in any case, 
>
> ./configure --with-freetype=system 
>
> should force sage to build freetype on its own.
>
>
>
>> Also, did you source .homebrew-build-env
>>> before doing ./configure && make ?
>>> As you use libraries from Homebrew, this might be crucial.
>>>
>>
>> I did that and it still does not work. See
>>
>> https://www.math.ucdavis.edu/~anne/config.log 
>> 
>>
>> Is it possible that this might be an issue
>>
>> https://github.com/Homebrew/legacy-homebrew/issues/43471
>>
>>
>> -- 
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>> "sage-devel" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to sage-devel+...@googlegroups.com.
>>
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>> https://groups.google.com/d/msgid/sage-devel/6ec9e78d-fd63-4122-91b2-d4600836aee8o%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [sage-devel] Problem building R on 10.15.5 with homebrew

[Zachary Scherr]

Hi Dima,

   It looks like both were already linked but I ended up reinstalling them 
and everything worked, thank you so much.  

In general, do you recommend installing libraries like flint from 
sagemath/homebrew-science before building sage? I see that there are a lot 
of formulas there but I'm not sure any of them have Catalina bottles.  I 
don't know too much about homebrew, but I'd be happy to try to contribute 
Catalina bottles if this is something worth doing. 

Best,
Zach


On Monday, June 1, 2020 at 3:51:23 PM UTC-4, Dima Pasechnik wrote:
>
> On Mon, Jun 1, 2020 at 8:30 PM Zachary Scherr  > wrote: 
> > 
> > Hi Dima, 
> > 
> >I already have all of the homebrew packages installed, I'm not sure 
> why it offers that suggestion. 
>
> By looking at your config.log, I see that flint and ntl are keg-only, 
> which actually results in sqlite ,zlib, and curl tests failing 
> (because the tests for libcurl and libsqlite actually try to link and 
> run programs linked to an already detected list of libs, 
> but locations of some of these libs need extra -L flags, oops) 
>
> brew link ntl 
> brew link flint 
> make zlib-clean sqlite-clean python3-clean 
>
> run 
> ./configure 
> it should tell you that zlib, sqlite, python3, r should come from the 
> system... 
>
>
>
>
> >  I also updated from OS 10.14 to 10.15 right before building sage.  I 
> had previously built sage on 10.14 without these problems. 
> > 
> > Best, 
> > Zach 
> > 
> > On Monday, June 1, 2020 at 3:27:19 PM UTC-4, Dima Pasechnik wrote: 
> >> 
> >> On Mon, Jun 1, 2020 at 7:37 PM Zachary Scherr  
> wrote: 
> >> > 
> >> > Hi All, 
> >> > 
> >> >I recently tried building Sage on Catalina 10.15.5.  I have 
> homebrew with all recommended packages installed and I tried building sage 
> via the commands 
> >> > 
> >> your config.log says that e.g. sqlite is not installed. 
> >> At the end of ./configure run, please have a look at the advice to 
> >> install packages it now prints. 
> >> 
> >> > make distclean 
> >> > source .homebrew-build-env 
> >> > ./configure 
> >> > MAKE='make -j18' make build 
> >> > 
> >> >and it crashed with the error 
> >> > 
> >> > Error building Sage. 
> >> > 
> >> > The following package(s) may have failed to build (not necessarily 
> >> > during this run of 'make all-build'): 
> >> > 
> >> > * package: r-3.6.2.p0 
> >> >   last build time: Jun 1 14:21 
> >> >   log file:/Users/zscherr/SageMath/logs/pkgs/r-3.6.2.p0.log 
> >> >   build directory: 
> /Users/zscherr/SageMath/local/var/tmp/sage/build/r-3.6.2.p0 
> >> > 
> >> >I'm not entirely sure why it's building R in the first place since 
> I already have it installed via homebrew.  I briefly checked the log file 
> and saw ld: library not found for -lssl which I'm thinking might be somehow 
> related 
> >> > to the fact that openssl and curl-openssl are keg-only.  My best 
> guess might be that "source .homebrew-build-env" ends up missing some 
> environment variables, but I'd really appreciate any help you can offer. 
> >> > 
> >> > Thanks, 
> >> > Zach 
> >> > 
> >> > -- 
> >> > 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-...@googlegroups.com. 
> >> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/6a84dd22-2e9e-4139-aab7-6582cb0bf598%40googlegroups.com.
>  
>
> > 
> > -- 
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> Groups "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-...@googlegroups.com . 
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>  
>
>

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Re: [sage-devel] Problem building R on 10.15.5 with homebrew

[Zachary Scherr]

Hi Dima,

   I already have all of the homebrew packages installed, I'm not sure why 
it offers that suggestion.  I also updated from OS 10.14 to 10.15 right 
before building sage.  I had previously built sage on 10.14 without these 
problems.

Best,
Zach

On Monday, June 1, 2020 at 3:27:19 PM UTC-4, Dima Pasechnik wrote:
>
> On Mon, Jun 1, 2020 at 7:37 PM Zachary Scherr  > wrote: 
> > 
> > Hi All, 
> > 
> >I recently tried building Sage on Catalina 10.15.5.  I have homebrew 
> with all recommended packages installed and I tried building sage via the 
> commands 
> > 
> your config.log says that e.g. sqlite is not installed. 
> At the end of ./configure run, please have a look at the advice to 
> install packages it now prints. 
>
> > make distclean 
> > source .homebrew-build-env 
> > ./configure 
> > MAKE='make -j18' make build 
> > 
> >and it crashed with the error 
> > 
> > Error building Sage. 
> > 
> > The following package(s) may have failed to build (not necessarily 
> > during this run of 'make all-build'): 
> > 
> > * package: r-3.6.2.p0 
> >   last build time: Jun 1 14:21 
> >   log file:/Users/zscherr/SageMath/logs/pkgs/r-3.6.2.p0.log 
> >   build directory: 
> /Users/zscherr/SageMath/local/var/tmp/sage/build/r-3.6.2.p0 
> > 
> >I'm not entirely sure why it's building R in the first place since I 
> already have it installed via homebrew.  I briefly checked the log file and 
> saw ld: library not found for -lssl which I'm thinking might be somehow 
> related 
> > to the fact that openssl and curl-openssl are keg-only.  My best guess 
> might be that "source .homebrew-build-env" ends up missing some environment 
> variables, but I'd really appreciate any help you can offer. 
> > 
> > Thanks, 
> > Zach 
> > 
> > -- 
> > 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-...@googlegroups.com . 
> > To view this discussion on the web visit 
> https://groups.google.com/d/msgid/sage-devel/6a84dd22-2e9e-4139-aab7-6582cb0bf598%40googlegroups.com.
>  
>
>

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[sage-devel] rpy2 fails to build when adding openssl to MacOS prebuilt sage 9 binary

[Zachary Scherr]

Hi,

   I recently tried adding openssl to the app.dmg prebuilt sage 9 binary 
via: sage -i openssl && sage -f python3.  During the rebuild, rpy2 failed 
with the message:

[rpy2-2.8.2.p1] dyld: lazy symbol binding failed: Symbol not found: 
_timespec_get
[rpy2-2.8.2.p1]   Referenced from: 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib
[rpy2-2.8.2.p1]   Expected in: /usr/lib/libSystem.B.dylib
[rpy2-2.8.2.p1]
[rpy2-2.8.2.p1] dyld: Symbol not found: _timespec_get
[rpy2-2.8.2.p1]   Referenced from: 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/R/lib/libR.dylib
[rpy2-2.8.2.p1]   Expected in: /usr/lib/libSystem.B.dylib

   From Googling, it appears that the problem might be tied to changes made 
by Xcode 11.  I will try to downgrade to Xcode 10 to see if this fixes the 
problem.  For what it's worth I am currently able to build sage from 
scratch, it's just that rebuilding is a problem.

Thanks,
Zach

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Found local metadata for rpy2-2.8.2.p1
Attempting to download package rpy2-2.8.2.tar.gz from mirrors
http://mirrors.mit.edu/sage/spkg/upstream/rpy2/rpy2-2.8.2.tar.gz
[..]
rpy2-2.8.2.p1

Setting up build directory for rpy2-2.8.2.p1
Finished extraction
Applying patches from ../patches...
Applying ../patches/cygwin.patch
patching file rpy/rinterface/na_values.c
patching file rpy/rinterface/_rinterface.c
Hunk #1 succeeded at 1156 (offset -6 lines).
Hunk #2 succeeded at 3750 (offset 1 line).
Hunk #3 succeeded at 3760 (offset 1 line).
Hunk #4 succeeded at 3770 (offset 1 line).
Hunk #5 succeeded at 3780 (offset 1 line).
patching file setup.py
Hunk #1 succeeded at 200 (offset 40 lines).

Host system:
Darwin Zacharys-MBP.fios-router.home 18.7.0 Darwin Kernel Version 18.7.0: Sun 
Dec  1 18:59:03 PST 2019; root:xnu-4903.278.19~1/RELEASE_X86_64 x86_64

C compiler: gcc
C compiler version:
Configured with: --prefix=/Library/Developer/CommandLineTools/usr 
--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Uninstalling existing 'rpy2'
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_dplyr.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_ggplot2.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__/test_grdevices.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/robjects/lib/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/interactive/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/ipython/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/ipython/tests/__pycache__/test_rmagic.cpython-37.pyc'
 not found
Warning: Directory 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/ipython/tests/__pycache__'
 not found
Warning: File 
'/Applications/SageMath-9.0.app/Contents/Resources/sage/local/lib/python3.7/site-packages/rpy2/rinterface/tests/__pycache__/__init__.cpython-37.pyc'
 not found
Warning: File 

Re: [sage-devel] scipy fails to build Sage 8.9 - MacOS 10.14.6

[Zachary Scherr]

Hi Dima,

   Just wanted to give you an update that Isuru's suggested fix also worked 
for me.  I have Xcode installed and have the directory

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk

and a 
symlink 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
 
to this directory.

I downloaded Isuru's suggested file and moved it 
to 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk,
 
and now everything works.

I'm guessing I could have just symlinked MacOSX10.14.sdk to MacOSX.sdk and 
everything would have worked, but I have not tested this yet.

Best,
Zach


 

On Wednesday, October 9, 2019 at 12:00:51 AM UTC-4, Dima Pasechnik wrote:
>
> I think there is no need to make Homebrew build gcc from source. (and 
> again, you only need gfortran, so make sure there is no "real" gcc in your 
> PATH)
> It's much more likely just the problem of using a binary built of Sage. 
>
> On Tue, Oct 8, 2019 at 10:47 PM Zachary Scherr  > wrote:
>
>> Will do. It also occurs to me that maybe I should force Homebrew to build 
>> GCC from source first and see if that works.  I'll experiment some more and 
>> let you know how it goes. Thank you for the help.
>>
>> On Tuesday, October 8, 2019 at 11:44:53 PM UTC-4, Dima Pasechnik wrote:
>>>
>>> Note that Ben was building Sage from source, whereas you're trying to 
>>> modify a binary Sage installation, something that is more error-prone.
>>> Would you mind trying to build from source instead?
>>>
>>>
>>> On Tue, Oct 8, 2019 at 10:22 PM Zachary Scherr  wrote:
>>>
>>>> That makes sense. I also tried installing gcc@8 and symlinking gfortran 
>>>> to make it point to the older version, but everything I've tried fails at 
>>>> the same point.
>>>>
>>>> On Tuesday, October 8, 2019 at 7:14:49 PM UTC-4, Dima Pasechnik wrote:
>>>>>
>>>>> No, you do NOT need "proper" gcc to build Sage on OSX, you need OSX's 
>>>>> clang/clang++
>>>>> OSX in its infinite wisdom aliases clang to gcc.
>>>>>
>>>>> One cannot build Sage on OSX with "real" gcc.
>>>>> That is, your "gcc" should be /usr/bin/gcc, which is actually clang.
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Oct 8, 2019 at 5:56 PM Zachary Scherr  
>>>>> wrote:
>>>>>
>>>>>> Hi Dima,
>>>>>>
>>>>>>I have, but I noticed something interesting which is that gcc and 
>>>>>> g++ are no longer symlinked in my /usr/local/bin.  I have gcc-9 and 
>>>>>> g++-9 
>>>>>> in there, but when I try "which gcc" and "which g++" I get /usr/bin/gcc 
>>>>>> and 
>>>>>> /usr/bin/g++ which are the versions installed by command line tools.  
>>>>>> This 
>>>>>> is making me even more confused because sage didn't even attempt to 
>>>>>> build 
>>>>>> with the version of gcc installed by homebrew.
>>>>>>
>>>>>>I'm currently retesting with gcc and g++ symlinked to the new 
>>>>>> version.  I'll let you know if I have any success.
>>>>>>
>>>>>> Thanks,
>>>>>> Zach  
>>>>>>
>>>>>> On Tuesday, October 8, 2019 at 4:25:23 PM UTC-4, Dima Pasechnik wrote:
>>>>>>>
>>>>>>> did you try updating homebrew?
>>>>>>>
>>>>>>> I think that what ultimately helped Ben to get a working gfortran, 
>>>>>>> and correctly build whatever scipy's dependency is causing the problem.
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Oct 8, 2019 at 3:17 PM Zachary Scherr  
>>>>>>> wrote:
>>>>>>>
>>>>>>>> In an attempt to add openssl to sage I ran: sage -i openssl && sage 
>>>>>>>> -f python2 (which I've done successfully in every previous version of 
>>>>>>>> Sage 
>>>>>>>> 8.x).
>>>>>>>>
>>>>>>>> The sage -f python2 failed while trying to build scipy-1.2.0.  This 
>>>>>>>> may be related to Ben's post 
>>>>>>>> https://groups.google.com/forum/#!topic/sage-devel/40E66JVHhW8 
>>>&g

Re: [sage-devel] scipy fails to build Sage 8.9 - MacOS 10.14.6

[Zachary Scherr]

Will do. It also occurs to me that maybe I should force Homebrew to build 
GCC from source first and see if that works.  I'll experiment some more and 
let you know how it goes. Thank you for the help.

On Tuesday, October 8, 2019 at 11:44:53 PM UTC-4, Dima Pasechnik wrote:
>
> Note that Ben was building Sage from source, whereas you're trying to 
> modify a binary Sage installation, something that is more error-prone.
> Would you mind trying to build from source instead?
>
>
> On Tue, Oct 8, 2019 at 10:22 PM Zachary Scherr  > wrote:
>
>> That makes sense. I also tried installing gcc@8 and symlinking gfortran 
>> to make it point to the older version, but everything I've tried fails at 
>> the same point.
>>
>> On Tuesday, October 8, 2019 at 7:14:49 PM UTC-4, Dima Pasechnik wrote:
>>>
>>> No, you do NOT need "proper" gcc to build Sage on OSX, you need OSX's 
>>> clang/clang++
>>> OSX in its infinite wisdom aliases clang to gcc.
>>>
>>> One cannot build Sage on OSX with "real" gcc.
>>> That is, your "gcc" should be /usr/bin/gcc, which is actually clang.
>>>
>>>
>>>
>>> On Tue, Oct 8, 2019 at 5:56 PM Zachary Scherr  wrote:
>>>
>>>> Hi Dima,
>>>>
>>>>I have, but I noticed something interesting which is that gcc and 
>>>> g++ are no longer symlinked in my /usr/local/bin.  I have gcc-9 and g++-9 
>>>> in there, but when I try "which gcc" and "which g++" I get /usr/bin/gcc 
>>>> and 
>>>> /usr/bin/g++ which are the versions installed by command line tools.  This 
>>>> is making me even more confused because sage didn't even attempt to build 
>>>> with the version of gcc installed by homebrew.
>>>>
>>>>I'm currently retesting with gcc and g++ symlinked to the new 
>>>> version.  I'll let you know if I have any success.
>>>>
>>>> Thanks,
>>>> Zach  
>>>>
>>>> On Tuesday, October 8, 2019 at 4:25:23 PM UTC-4, Dima Pasechnik wrote:
>>>>>
>>>>> did you try updating homebrew?
>>>>>
>>>>> I think that what ultimately helped Ben to get a working gfortran, and 
>>>>> correctly build whatever scipy's dependency is causing the problem.
>>>>>
>>>>>
>>>>> On Tue, Oct 8, 2019 at 3:17 PM Zachary Scherr  
>>>>> wrote:
>>>>>
>>>>>> In an attempt to add openssl to sage I ran: sage -i openssl && sage 
>>>>>> -f python2 (which I've done successfully in every previous version of 
>>>>>> Sage 
>>>>>> 8.x).
>>>>>>
>>>>>> The sage -f python2 failed while trying to build scipy-1.2.0.  This 
>>>>>> may be related to Ben's post 
>>>>>> https://groups.google.com/forum/#!topic/sage-devel/40E66JVHhW8 since 
>>>>>> it also failed with the message
>>>>>>
>>>>>> ld: library not found for -lSystem
>>>>>>
>>>>>> I too have gcc installed through homebrew, but I also tried removing 
>>>>>> it and installing gfortran separately and ended up with the same error.  
>>>>>> I've attached the log file, anyone know what's going on?
>>>>>>
>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> 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-...@googlegroups.com.
>>>>>> To view this discussion on the web visit 
>>>>>> https://groups.google.com/d/msgid/sage-devel/5a356d10-a069-487a-a75c-ace33ba11f07%40googlegroups.com
>>>>>>  
>>>>>> <https://groups.google.com/d/msgid/sage-devel/5a356d10-a069-487a-a75c-ace33ba11f07%40googlegroups.com?utm_medium=email_source=footer>
>>>>>> .
>>>>>>
>>>>> -- 
>>>> 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-...@googlegroups.com.
>>>> To view this discussion on the web visit 
>>>> https://groups.google.com/d/msgid/sage-devel/cd8fa4be-df55-42a4-aeb3-d747fc42fbda%40googlegroups.com
>>>>  
>>>> <https://groups.google.com/d/msgid/sage-devel/cd8fa4be-df55-42a4-aeb3-d747fc42fbda%40googlegroups.com?utm_medium=email_source=footer>
>>>> .
>>>>
>>> -- 
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>> email to sage-...@googlegroups.com .
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>>  
>> <https://groups.google.com/d/msgid/sage-devel/8847eaa7-389c-49d8-b9d2-09d696e2a4b8%40googlegroups.com?utm_medium=email_source=footer>
>> .
>>
>

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Re: [sage-devel] scipy fails to build Sage 8.9 - MacOS 10.14.6

[Zachary Scherr]

That makes sense. I also tried installing gcc@8 and symlinking gfortran to 
make it point to the older version, but everything I've tried fails at the 
same point.

On Tuesday, October 8, 2019 at 7:14:49 PM UTC-4, Dima Pasechnik wrote:
>
> No, you do NOT need "proper" gcc to build Sage on OSX, you need OSX's 
> clang/clang++
> OSX in its infinite wisdom aliases clang to gcc.
>
> One cannot build Sage on OSX with "real" gcc.
> That is, your "gcc" should be /usr/bin/gcc, which is actually clang.
>
>
>
> On Tue, Oct 8, 2019 at 5:56 PM Zachary Scherr  > wrote:
>
>> Hi Dima,
>>
>>I have, but I noticed something interesting which is that gcc and g++ 
>> are no longer symlinked in my /usr/local/bin.  I have gcc-9 and g++-9 in 
>> there, but when I try "which gcc" and "which g++" I get /usr/bin/gcc and 
>> /usr/bin/g++ which are the versions installed by command line tools.  This 
>> is making me even more confused because sage didn't even attempt to build 
>> with the version of gcc installed by homebrew.
>>
>>I'm currently retesting with gcc and g++ symlinked to the new 
>> version.  I'll let you know if I have any success.
>>
>> Thanks,
>> Zach  
>>
>> On Tuesday, October 8, 2019 at 4:25:23 PM UTC-4, Dima Pasechnik wrote:
>>>
>>> did you try updating homebrew?
>>>
>>> I think that what ultimately helped Ben to get a working gfortran, and 
>>> correctly build whatever scipy's dependency is causing the problem.
>>>
>>>
>>> On Tue, Oct 8, 2019 at 3:17 PM Zachary Scherr  wrote:
>>>
>>>> In an attempt to add openssl to sage I ran: sage -i openssl && sage -f 
>>>> python2 (which I've done successfully in every previous version of Sage 
>>>> 8.x).
>>>>
>>>> The sage -f python2 failed while trying to build scipy-1.2.0.  This may 
>>>> be related to Ben's post 
>>>> https://groups.google.com/forum/#!topic/sage-devel/40E66JVHhW8 since 
>>>> it also failed with the message
>>>>
>>>> ld: library not found for -lSystem
>>>>
>>>> I too have gcc installed through homebrew, but I also tried removing it 
>>>> and installing gfortran separately and ended up with the same error.  I've 
>>>> attached the log file, anyone know what's going on?
>>>>
>>>>
>>>>
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>>>>  
>>>> <https://groups.google.com/d/msgid/sage-devel/5a356d10-a069-487a-a75c-ace33ba11f07%40googlegroups.com?utm_medium=email_source=footer>
>>>> .
>>>>
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Re: [sage-devel] scipy fails to build Sage 8.9 - MacOS 10.14.6

[Zachary Scherr]

Hi Dima,

   I have, but I noticed something interesting which is that gcc and g++ 
are no longer symlinked in my /usr/local/bin.  I have gcc-9 and g++-9 in 
there, but when I try "which gcc" and "which g++" I get /usr/bin/gcc and 
/usr/bin/g++ which are the versions installed by command line tools.  This 
is making me even more confused because sage didn't even attempt to build 
with the version of gcc installed by homebrew.

   I'm currently retesting with gcc and g++ symlinked to the new version. 
 I'll let you know if I have any success.

Thanks,
Zach  

On Tuesday, October 8, 2019 at 4:25:23 PM UTC-4, Dima Pasechnik wrote:
>
> did you try updating homebrew?
>
> I think that what ultimately helped Ben to get a working gfortran, and 
> correctly build whatever scipy's dependency is causing the problem.
>
>
> On Tue, Oct 8, 2019 at 3:17 PM Zachary Scherr  > wrote:
>
>> In an attempt to add openssl to sage I ran: sage -i openssl && sage -f 
>> python2 (which I've done successfully in every previous version of Sage 
>> 8.x).
>>
>> The sage -f python2 failed while trying to build scipy-1.2.0.  This may 
>> be related to Ben's post 
>> https://groups.google.com/forum/#!topic/sage-devel/40E66JVHhW8 since it 
>> also failed with the message
>>
>> ld: library not found for -lSystem
>>
>> I too have gcc installed through homebrew, but I also tried removing it 
>> and installing gfortran separately and ended up with the same error.  I've 
>> attached the log file, anyone know what's going on?
>>
>>
>>
>> -- 
>> 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-...@googlegroups.com .
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/sage-devel/5a356d10-a069-487a-a75c-ace33ba11f07%40googlegroups.com
>>  
>> <https://groups.google.com/d/msgid/sage-devel/5a356d10-a069-487a-a75c-ace33ba11f07%40googlegroups.com?utm_medium=email_source=footer>
>> .
>>
>

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