[sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

On Wednesday, April 1, 2020 at 3:02:49 PM UTC-7, Matthias Köppe wrote:
>
> Another variation to try is to use " . .homebrew-build-env "
> before the build, which sets some environment variables so that homebrew's 
> "keg-only packages" are found.  
> Among other things, this affects libpng via zlib.
>

I think that when homebrew is detected, the "hints" at the end of 
./configure should recommend "source .homebrew-build-env" or similar. See 
trac #29504.

  John

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

Another variation to try is to use " . .homebrew-build-env "
before the build, which sets some environment variables so that homebrew's 
"keg-only packages" are found.  
Among other things, this affects libpng via zlib.


On Wednesday, April 1, 2020 at 2:05:31 PM UTC-4, John H Palmieri wrote:
>
>
>
> On Tuesday, March 31, 2020 at 7:15:10 PM UTC-7, John H Palmieri wrote:
>>
>>
>>
>> On Tuesday, March 31, 2020 at 6:21:42 PM UTC-7, Matthias Köppe wrote:
>>>
>>> On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote:

 Here's the strange part: if I add the package libpng, then Sage doesn't 
 build. With these packages, it builds and passes tests (output from "brew 
 list --versions"):

 autoconf 2.69
 automake 1.16.2
 boost 1.72.0_1
 cabextract 1.9.1
 emacs-mac emacs-26.3-z-mac-7.9
 gcc 9.2.0_1 9.3.0
 gdbm 1.18.1
 gettext 0.20.1
 gmp 6.2.0 6.1.2_2
 gnutls 3.6.12
 icu4c 64.2
 isl 0.22.1 0.21 0.18
 jpeg 9d
 libdvdcss 1.4.2
 libevent 2.1.11_1
 libffi 3.2.1
 libidn2 2.3.0
 libmpc 1.1.0
 libtasn1 4.14 4.16.0
 libtiff 4.1.0
 libunistring 0.9.10
 mpfr 4.0.2
 nettle 3.4.1
 openssl@1.1 1.1.1d
 p11-kit 0.23.20 0.23.18.1
 pkg-config 0.29.2
 readline 8.0.4
 sqlite 3.31.1
 unbound 1.9.4 1.10.0
 xz 5.2.5

>>>
>>> python3's spkg-configure refuses to use system python if we install any 
>>> of the following from spkg:
>>>
>>> sqlite libpng bzip2 xz libffi
>>>
>>> bzip2 comes from /usr/bin
>>> The others from homebrew.
>>> When you install libpng in addition to the list of packages, the set of 
>>> prerequisites for accepting system python3 is complete, and then the 
>>> unresolved problems with the build (kiwisolver, ...) appear when system 
>>> python 3 is /usr/bin/python3 (XCode's python3).
>>>
>>> It does not happen if you have homebrew python3 in PATH. 
>>>
>>
>> Right, I realized that, too. However, I initially had even more homebrew 
>> packages installed, Sage built using the system Python, and the build 
>> succeeded. That's when I ran into the doctest failures, which I am now 
>> trying to reproduce: trying to see which homebrew packages trigger them.
>>
>>
> To summarize:
>
> - if I don't install libpng (for example), then Sage builds its own Python 
> and everything works, all tests pass.
> - if I don't install Homebrew's python but enough other packages, then the 
> OS X Python is used, and kiwisolver fails to build. Trac 29408 appears to 
> help with that; I'm trying a full build now.
> - if I install Homebrew's python but not pkg-config, then matplotlib fails 
> to build because it can't find libpng. (The top-level configure script 
> finds it and so decides not to build it.)
> - if I also install pkg-config, the build succeeds but I get all of the 
> doctest failures I reported before. In this last case, here's what I've 
> installed — I tried to keep the list as small as possible:
>
> gcc 9.2.0_1 9.3.0
> gdbm 1.18.1
> gmp 6.2.0 6.1.2_2
> isl 0.22.1 0.21 0.18
> libmpc 1.1.0
> libpng 1.6.37
> libunistring 0.9.10
> mpfr 4.0.2
> openssl@1.1 1.1.1d
> pkg-config 0.29.2
> python 3.7.7
> readline 8.0.4
> sqlite 3.31.1
> xz 5.2.5 
>
> Overall, this is a precarious situation.
>
> By the way, this is with OS X 10.15.4 and the latest Xcode,
>
> % gcc --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 11.0.3 (clang-1103.0.32.29)
> Target: x86_64-apple-darwin19.4.0
> Thread model: posix
> InstalledDir: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>
>

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[sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

On Wednesday, April 1, 2020 at 11:05:31 AM UTC-7, John H Palmieri wrote:
>
>
>
> On Tuesday, March 31, 2020 at 7:15:10 PM UTC-7, John H Palmieri wrote:
>>
>>
>>
>> On Tuesday, March 31, 2020 at 6:21:42 PM UTC-7, Matthias Köppe wrote:
>>>
>>> On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote:

 Here's the strange part: if I add the package libpng, then Sage doesn't 
 build. With these packages, it builds and passes tests (output from "brew 
 list --versions"):

 autoconf 2.69
 automake 1.16.2
 boost 1.72.0_1
 cabextract 1.9.1
 emacs-mac emacs-26.3-z-mac-7.9
 gcc 9.2.0_1 9.3.0
 gdbm 1.18.1
 gettext 0.20.1
 gmp 6.2.0 6.1.2_2
 gnutls 3.6.12
 icu4c 64.2
 isl 0.22.1 0.21 0.18
 jpeg 9d
 libdvdcss 1.4.2
 libevent 2.1.11_1
 libffi 3.2.1
 libidn2 2.3.0
 libmpc 1.1.0
 libtasn1 4.14 4.16.0
 libtiff 4.1.0
 libunistring 0.9.10
 mpfr 4.0.2
 nettle 3.4.1
 openssl@1.1 1.1.1d
 p11-kit 0.23.20 0.23.18.1
 pkg-config 0.29.2
 readline 8.0.4
 sqlite 3.31.1
 unbound 1.9.4 1.10.0
 xz 5.2.5

>>>
>>> python3's spkg-configure refuses to use system python if we install any 
>>> of the following from spkg:
>>>
>>> sqlite libpng bzip2 xz libffi
>>>
>>> bzip2 comes from /usr/bin
>>> The others from homebrew.
>>> When you install libpng in addition to the list of packages, the set of 
>>> prerequisites for accepting system python3 is complete, and then the 
>>> unresolved problems with the build (kiwisolver, ...) appear when system 
>>> python 3 is /usr/bin/python3 (XCode's python3).
>>>
>>> It does not happen if you have homebrew python3 in PATH. 
>>>
>>
>> Right, I realized that, too. However, I initially had even more homebrew 
>> packages installed, Sage built using the system Python, and the build 
>> succeeded. That's when I ran into the doctest failures, which I am now 
>> trying to reproduce: trying to see which homebrew packages trigger them.
>>
>>
> To summarize:
>
> - if I don't install libpng (for example), then Sage builds its own Python 
> and everything works, all tests pass.
> - if I don't install Homebrew's python but enough other packages, then the 
> OS X Python is used, and kiwisolver fails to build. Trac 29408 appears to 
> help with that; I'm trying a full build now.
>

With trac 29404 + 29408, the build succeeds with the system python, but I 
get many of the doctest failures that arise with Homebrew's python.
 

> - if I install Homebrew's python but not pkg-config, then matplotlib fails 
> to build because it can't find libpng. (The top-level configure script 
> finds it and so decides not to build it.)
> - if I also install pkg-config, the build succeeds but I get all of the 
> doctest failures I reported before. In this last case, here's what I've 
> installed — I tried to keep the list as small as possible:
>
> gcc 9.2.0_1 9.3.0
> gdbm 1.18.1
> gmp 6.2.0 6.1.2_2
> isl 0.22.1 0.21 0.18
> libmpc 1.1.0
> libpng 1.6.37
> libunistring 0.9.10
> mpfr 4.0.2
> openssl@1.1 1.1.1d
> pkg-config 0.29.2
> python 3.7.7
> readline 8.0.4
> sqlite 3.31.1
> xz 5.2.5 
>
> Overall, this is a precarious situation.
>
> By the way, this is with OS X 10.15.4 and the latest Xcode,
>
> % gcc --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 11.0.3 (clang-1103.0.32.29)
> Target: x86_64-apple-darwin19.4.0
> Thread model: posix
> InstalledDir: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>
>

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[sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

On Tuesday, March 31, 2020 at 7:15:10 PM UTC-7, John H Palmieri wrote:
>
>
>
> On Tuesday, March 31, 2020 at 6:21:42 PM UTC-7, Matthias Köppe wrote:
>>
>> On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote:
>>>
>>> Here's the strange part: if I add the package libpng, then Sage doesn't 
>>> build. With these packages, it builds and passes tests (output from "brew 
>>> list --versions"):
>>>
>>> autoconf 2.69
>>> automake 1.16.2
>>> boost 1.72.0_1
>>> cabextract 1.9.1
>>> emacs-mac emacs-26.3-z-mac-7.9
>>> gcc 9.2.0_1 9.3.0
>>> gdbm 1.18.1
>>> gettext 0.20.1
>>> gmp 6.2.0 6.1.2_2
>>> gnutls 3.6.12
>>> icu4c 64.2
>>> isl 0.22.1 0.21 0.18
>>> jpeg 9d
>>> libdvdcss 1.4.2
>>> libevent 2.1.11_1
>>> libffi 3.2.1
>>> libidn2 2.3.0
>>> libmpc 1.1.0
>>> libtasn1 4.14 4.16.0
>>> libtiff 4.1.0
>>> libunistring 0.9.10
>>> mpfr 4.0.2
>>> nettle 3.4.1
>>> openssl@1.1 1.1.1d
>>> p11-kit 0.23.20 0.23.18.1
>>> pkg-config 0.29.2
>>> readline 8.0.4
>>> sqlite 3.31.1
>>> unbound 1.9.4 1.10.0
>>> xz 5.2.5
>>>
>>
>> python3's spkg-configure refuses to use system python if we install any 
>> of the following from spkg:
>>
>> sqlite libpng bzip2 xz libffi
>>
>> bzip2 comes from /usr/bin
>> The others from homebrew.
>> When you install libpng in addition to the list of packages, the set of 
>> prerequisites for accepting system python3 is complete, and then the 
>> unresolved problems with the build (kiwisolver, ...) appear when system 
>> python 3 is /usr/bin/python3 (XCode's python3).
>>
>> It does not happen if you have homebrew python3 in PATH. 
>>
>
> Right, I realized that, too. However, I initially had even more homebrew 
> packages installed, Sage built using the system Python, and the build 
> succeeded. That's when I ran into the doctest failures, which I am now 
> trying to reproduce: trying to see which homebrew packages trigger them.
>
>
To summarize:

- if I don't install libpng (for example), then Sage builds its own Python 
and everything works, all tests pass.
- if I don't install Homebrew's python but enough other packages, then the 
OS X Python is used, and kiwisolver fails to build. Trac 29408 appears to 
help with that; I'm trying a full build now.
- if I install Homebrew's python but not pkg-config, then matplotlib fails 
to build because it can't find libpng. (The top-level configure script 
finds it and so decides not to build it.)
- if I also install pkg-config, the build succeeds but I get all of the 
doctest failures I reported before. In this last case, here's what I've 
installed — I tried to keep the list as small as possible:

gcc 9.2.0_1 9.3.0
gdbm 1.18.1
gmp 6.2.0 6.1.2_2
isl 0.22.1 0.21 0.18
libmpc 1.1.0
libpng 1.6.37
libunistring 0.9.10
mpfr 4.0.2
openssl@1.1 1.1.1d
pkg-config 0.29.2
python 3.7.7
readline 8.0.4
sqlite 3.31.1
xz 5.2.5 

Overall, this is a precarious situation.

By the way, this is with OS X 10.15.4 and the latest Xcode,

% gcc --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 11.0.3 (clang-1103.0.32.29)
Target: x86_64-apple-darwin19.4.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

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Re: [sage-release] Re: Sage 9.1.beta9 released

[Markus Wageringel]

> Am 31.03.2020 um 23:25 schrieb Matthias Köppe :
> 
> That is, the file `local/bin/sage-starts` is not found. This is with CentOS 
> 7.7.
> 
> 
> This script was moved in https://trac.sagemath.org/ticket/23769 
> 
It looks like the patchbot needs to be updated for this. I will send a pull 
request, shortly.

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Re: [sage-release] Re: Sage 9.1.beta9 released

[Markus Wageringel]

> Am 31.03.2020 um 23:30 schrieb Matthias Köppe :
> Looks like this new doctest (from https://trac.sagemath.org/ticket/29287) 
> needs some os.path.abspath in it. Please open a ticket for this.

Ok, I have opened https://trac.sagemath.org/ticket/29446 
 for this. I had not realized this was 
a new doctest.

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[sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

On Tuesday, March 31, 2020 at 6:21:42 PM UTC-7, Matthias Köppe wrote:
>
> On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote:
>>
>> Here's the strange part: if I add the package libpng, then Sage doesn't 
>> build. With these packages, it builds and passes tests (output from "brew 
>> list --versions"):
>>
>> autoconf 2.69
>> automake 1.16.2
>> boost 1.72.0_1
>> cabextract 1.9.1
>> emacs-mac emacs-26.3-z-mac-7.9
>> gcc 9.2.0_1 9.3.0
>> gdbm 1.18.1
>> gettext 0.20.1
>> gmp 6.2.0 6.1.2_2
>> gnutls 3.6.12
>> icu4c 64.2
>> isl 0.22.1 0.21 0.18
>> jpeg 9d
>> libdvdcss 1.4.2
>> libevent 2.1.11_1
>> libffi 3.2.1
>> libidn2 2.3.0
>> libmpc 1.1.0
>> libtasn1 4.14 4.16.0
>> libtiff 4.1.0
>> libunistring 0.9.10
>> mpfr 4.0.2
>> nettle 3.4.1
>> openssl@1.1 1.1.1d
>> p11-kit 0.23.20 0.23.18.1
>> pkg-config 0.29.2
>> readline 8.0.4
>> sqlite 3.31.1
>> unbound 1.9.4 1.10.0
>> xz 5.2.5
>>
>
> python3's spkg-configure refuses to use system python if we install any of 
> the following from spkg:
>
> sqlite libpng bzip2 xz libffi
>
> bzip2 comes from /usr/bin
> The others from homebrew.
> When you install libpng in addition to the list of packages, the set of 
> prerequisites for accepting system python3 is complete, and then the 
> unresolved problems with the build (kiwisolver, ...) appear when system 
> python 3 is /usr/bin/python3 (XCode's python3).
>
> It does not happen if you have homebrew python3 in PATH. 
>

Right, I realized that, too. However, I initially had even more homebrew 
packages installed, Sage built using the system Python, and the build 
succeeded. That's when I ran into the doctest failures, which I am now 
trying to reproduce: trying to see which homebrew packages trigger them.

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote:
>
> Here's the strange part: if I add the package libpng, then Sage doesn't 
> build. With these packages, it builds and passes tests (output from "brew 
> list --versions"):
>
> autoconf 2.69
> automake 1.16.2
> boost 1.72.0_1
> cabextract 1.9.1
> emacs-mac emacs-26.3-z-mac-7.9
> gcc 9.2.0_1 9.3.0
> gdbm 1.18.1
> gettext 0.20.1
> gmp 6.2.0 6.1.2_2
> gnutls 3.6.12
> icu4c 64.2
> isl 0.22.1 0.21 0.18
> jpeg 9d
> libdvdcss 1.4.2
> libevent 2.1.11_1
> libffi 3.2.1
> libidn2 2.3.0
> libmpc 1.1.0
> libtasn1 4.14 4.16.0
> libtiff 4.1.0
> libunistring 0.9.10
> mpfr 4.0.2
> nettle 3.4.1
> openssl@1.1 1.1.1d
> p11-kit 0.23.20 0.23.18.1
> pkg-config 0.29.2
> readline 8.0.4
> sqlite 3.31.1
> unbound 1.9.4 1.10.0
> xz 5.2.5
>

python3's spkg-configure refuses to use system python if we install any of 
the following from spkg:

sqlite libpng bzip2 xz libffi

bzip2 comes from /usr/bin
The others from homebrew.
When you install libpng in addition to the list of packages, the set of 
prerequisites for accepting system python3 is complete, and then the 
unresolved problems with the build (kiwisolver, ...) appear when system 
python 3 is /usr/bin/python3 (XCode's python3).

It does not happen if you have homebrew python3 in PATH. 



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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote:
>
> [...] 
>
kiwisolver fails to build. For some reason, something in the build process 
> thinks that "-sdk" is a good flag to add to "g++":
>
> g++ -sdk macosx clang -bundle -undefined dynamic_lookup 
> -L/Users/palmieri/Desktop/Sage_stuff/sage_builds/TESTING/png/sage-9.1.beta9/local/lib
>  
> -Wl,-rpath,/Users/palmieri/Desktop/Sage_stuff/sage_builds/TESTING/png/sage-9.1.beta9/local/lib
>  
> build/temp.macosx-10.14-x86_64-3.7/py/kiwisolver.o 
> build/temp.macosx-10.14-x86_64-3.7/py/constraint.o 
> build/temp.macosx-10.14-x86_64-3.7/py/expression.o 
> build/temp.macosx-10.14-x86_64-3.7/py/solver.o 
> build/temp.macosx-10.14-x86_64-3.7/py/strength.o 
> build/temp.macosx-10.14-x86_64-3.7/py/term.o 
> build/temp.macosx-10.14-x86_64-3.7/py/variable.o -o 
> build/lib.macosx-10.14-x86_64-3.7/kiwisolver.cpython-37m-darwin.so
> clang: error: unknown argument: '-sdk'
> clang: error: no such file or directory: 'macosx'
> clang: error: no such file or directory: 'clang'
> error: command 'g++' failed with exit status 1
>
> I didn't see this before, so if I add enough other packages, this problem 
> will somehow resolve itself. This is specific to 9.1.beta9 (i.e., using the 
> system python3): kiwisolver builds with 9.1.beta8 and these homebrew 
> packages.
>

This is https://trac.sagemath.org/ticket/29408


 

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[sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

Some good news and some weird news: in my attempts to debug this, I 
uninstalled a bunch of my homebrew packages, and I got Sage to build and 
pass tests. Yay. Here's the strange part: if I add the package libpng, then 
Sage doesn't build. With these packages, it builds and passes tests (output 
from "brew list --versions"):

autoconf 2.69
automake 1.16.2
boost 1.72.0_1
cabextract 1.9.1
emacs-mac emacs-26.3-z-mac-7.9
gcc 9.2.0_1 9.3.0
gdbm 1.18.1
gettext 0.20.1
gmp 6.2.0 6.1.2_2
gnutls 3.6.12
icu4c 64.2
isl 0.22.1 0.21 0.18
jpeg 9d
libdvdcss 1.4.2
libevent 2.1.11_1
libffi 3.2.1
libidn2 2.3.0
libmpc 1.1.0
libtasn1 4.14 4.16.0
libtiff 4.1.0
libunistring 0.9.10
mpfr 4.0.2
nettle 3.4.1
openssl@1.1 1.1.1d
p11-kit 0.23.20 0.23.18.1
pkg-config 0.29.2
readline 8.0.4
sqlite 3.31.1
unbound 1.9.4 1.10.0
xz 5.2.5

If I then do "brew install libpng" and build Sage from scratch, kiwisolver 
fails to build. For some reason, something in the build process thinks that 
"-sdk" is a good flag to add to "g++":

g++ -sdk macosx clang -bundle -undefined dynamic_lookup 
-L/Users/palmieri/Desktop/Sage_stuff/sage_builds/TESTING/png/sage-9.1.beta9/local/lib
 
-Wl,-rpath,/Users/palmieri/Desktop/Sage_stuff/sage_builds/TESTING/png/sage-9.1.beta9/local/lib
 
build/temp.macosx-10.14-x86_64-3.7/py/kiwisolver.o 
build/temp.macosx-10.14-x86_64-3.7/py/constraint.o 
build/temp.macosx-10.14-x86_64-3.7/py/expression.o 
build/temp.macosx-10.14-x86_64-3.7/py/solver.o 
build/temp.macosx-10.14-x86_64-3.7/py/strength.o 
build/temp.macosx-10.14-x86_64-3.7/py/term.o 
build/temp.macosx-10.14-x86_64-3.7/py/variable.o -o 
build/lib.macosx-10.14-x86_64-3.7/kiwisolver.cpython-37m-darwin.so
clang: error: unknown argument: '-sdk'
clang: error: no such file or directory: 'macosx'
clang: error: no such file or directory: 'clang'
error: command 'g++' failed with exit status 1

I didn't see this before, so if I add enough other packages, this problem 
will somehow resolve itself. This is specific to 9.1.beta9 (i.e., using the 
system python3): kiwisolver builds with 9.1.beta8 and these homebrew 
packages.


On Monday, March 30, 2020 at 3:59:30 PM UTC-7, John H Palmieri wrote:
>
> I see the same in the log file for the Python 2 build. I wonder if this 
> has to do with upgrading Xcode, which I seem to have done 6 days ago. To be 
> clear, yesterday and today I have built  9.1.beta8 + Python 3 and 9.1.beta9 
> + Python 2, both successfully, despite this crash. It's 9.1.beta9 + Python 
> 3 which is causing problems. It also seems to be using the Apple Python 3, 
> /usr/bin/python3, not the one installed by homebrew.
>
> For what it's worth:
>
> - I don't see this crash message from config.log files from a few weeks 
> ago.
> - the message refers to a file 
>
> /Users/palmieri/Library/Logs/DiagnosticReports/clang__.crash,
>
> but there is no such file.
>
>
>
> On Monday, March 30, 2020 at 1:44:41 PM UTC-7, Matthias Köppe wrote:
>>
>> From your config.log ... rather suspicious:
>>
>> configure:10189: g++ -std=gnu++11 -o conftest -g -O2   conftest.cpp -lgmp  
>> -lm  >&5
>> configure:10189: $? = 0
>> configure:10206: result: -lgmp
>> configure:10231: will use system package and not install SPKG mpir
>> configure:10265: checking absolute name of 
>> configure:10272: checking for gmp.h
>> configure:10272: result: yes
>> clang: error: unable to execute command: Broken pipe: 13
>> clang: error: clang frontend command failed due to signal (use -v to see 
>> invocation)
>> Apple clang version 11.0.3 (clang-1103.0.32.29)
>> Target: x86_64-apple-darwin19.3.0
>> Thread model: posix
>> InstalledDir: 
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>> clang: note: diagnostic msg: PLEASE submit a bug report to 
>> http://developer.apple.com/bugreporter/ and include the crash backtrace, 
>> preprocessed source, and associated run script.
>> clang: note: diagnostic msg: 
>> 
>>
>> PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
>> Preprocessed source(s) and associated run script(s) are located at:
>> clang: note: diagnostic msg: 
>> /var/folders/cp/n8wtqs490tq5psknff1hv9qrgn/T/conftest-d428b4.cpp
>> clang: note: diagnostic msg: 
>> /var/folders/cp/n8wtqs490tq5psknff1hv9qrgn/T/conftest-d428b4.sh
>> clang: note: diagnostic msg: Crash backtrace is located in
>> clang: note: diagnostic msg: 
>> /Users/palmieri/Library/Logs/DiagnosticReports/clang__.crash
>> clang: note: diagnostic msg: (choose the .crash file that corresponds to 
>> your crash)
>> clang: note: diagnostic msg: 
>>
>> 
>> configure:10296: result: ///usr/local/include/gmp.h
>> configure:10332: result: using GMP-compatible library from the system
>> ##  ##
>> ## Checking whether SageMath should install SPKG gmp... ##
>> ##  ##
>> configure:10415: will use system package and not install SPKG gmp
>>
>>
>>
>> 

[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Tuesday, March 31, 2020 at 1:40:19 PM UTC-4, Steven Trogdon wrote:
>
> I rebuilt Sage using the Sage-provided python instead my system python and 
> doctested Sage. The failure in doctest/test.py disappears. However, the 
> failures in rings/integer.pyx still persist. I suspect a system component 
> is the culprit. Any ideas which one? I had doctested 9.1.beta8 with no 
> failures, so something has changed.
>
>>
>>>
Sage is able to use more system packages compared to 9.1.beta8 (via the 
spkg-configure.m4 mechanism). I recommend to compare config.log with the 
one in the earlier build, checking messages regarding the system packages.

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Tuesday, March 31, 2020 at 4:18:08 PM UTC-4, Markus Wageringel wrote:
>
> Since this beta, I get the following permanent failure:
>
> sage -t --long src/sage/env.py
> **
> File "src/sage/env.py", line 15, in sage.env
> Failed example:
> out == repr((SAGE_ROOT, SAGE_LOCAL)) 
># long time
> Expected:
> True
> Got:
> False
>
> Here, SAGE_ROOT and SAGE_LOCAL look correct, but the `out` variable from 
> the preceding tests is
>
> sage: env = {k:v for (k,v) in os.environ.items() if not k.startswith(
> "SAGE_")}
> sage: from subprocess import check_output
> sage: cmd = "from sage.all import SAGE_ROOT, SAGE_LOCAL; 
> print((SAGE_ROOT, SAGE_LOCAL))"
> sage: out = check_output([sys.executable, "-c", cmd], env=env).decode
> ().strip()   # long time
> sage: out
> "('/home/math/sagebot/sage', '/amd/compute/sagebot/sage/local')"
>
> The left path is actually a symlink in my home directory to my sage root 
> directory on a different partition:
>
> sage: SAGE_ROOT
> '/amd/compute/sagebot/sage'
>
>
>
Looks like this new doctest (from https://trac.sagemath.org/ticket/29287) 
needs some os.path.abspath in it. Please open a ticket for this.
 

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Tuesday, March 31, 2020 at 4:18:08 PM UTC-4, Markus Wageringel wrote:
>
>  my patchbot failed multiple times with the following possibly related 
> error:
>
> ...
> Sage build/upgrade complete!
> make[1]: Verzeichnis „/amd/compute/sagebot/sage“ wird verlassen
> sh: /amd/compute/sagebot/sage/local/bin/sage-starts: Datei oder 
> Verzeichnis nicht gefunden
>
> That is, the file `local/bin/sage-starts` is not found. This is with 
> CentOS 7.7.
>
>
This script was moved in https://trac.sagemath.org/ticket/23769

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[sage-release] Re: Sage 9.1.beta9 released

[Markus Wageringel]

Since this beta, I get the following permanent failure:

sage -t --long src/sage/env.py
**
File "src/sage/env.py", line 15, in sage.env
Failed example:
out == repr((SAGE_ROOT, SAGE_LOCAL))   
 # long time
Expected:
True
Got:
False

Here, SAGE_ROOT and SAGE_LOCAL look correct, but the `out` variable from 
the preceding tests is

sage: env = {k:v for (k,v) in os.environ.items() if not k.startswith(
"SAGE_")}
sage: from subprocess import check_output
sage: cmd = "from sage.all import SAGE_ROOT, SAGE_LOCAL; 
print((SAGE_ROOT, SAGE_LOCAL))"
sage: out = check_output([sys.executable, "-c", cmd], env=env).decode().
strip()   # long time
sage: out
"('/home/math/sagebot/sage', '/amd/compute/sagebot/sage/local')"

The left path is actually a symlink in my home directory to my sage root 
directory on a different partition:

sage: SAGE_ROOT
'/amd/compute/sagebot/sage'

Moreover, my patchbot failed multiple times with the following possibly 
related error:

...
Sage build/upgrade complete!
make[1]: Verzeichnis „/amd/compute/sagebot/sage“ wird verlassen
sh: /amd/compute/sagebot/sage/local/bin/sage-starts: Datei oder 
Verzeichnis nicht gefunden

That is, the file `local/bin/sage-starts` is not found. This is with CentOS 
7.7.

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[sage-release] Re: Sage 9.1.beta9 released

[Markus Wageringel]

I also see the error in rings/integer.pyx again now. This is 
https://trac.sagemath.org/ticket/28106. The doctests are limited to 3300 MB 
of memory be default, but this test exceeds it. The limit can be manually 
increased using the `--memlimit` option.


Am Dienstag, 31. März 2020 19:40:19 UTC+2 schrieb Steven Trogdon:
>
> I'm replying to my previous post.
>
> I rebuilt Sage using the Sage-provided python instead my system python and 
> doctested Sage. The failure in doctest/test.py disappears. However, the 
> failures in rings/integer.pyx still persist. I suspect a system component 
> is the culprit. Any ideas which one? I had doctested 9.1.beta8 with no 
> failures, so something has changed.
>
> On Monday, March 30, 2020 at 4:54:19 PM UTC-5, Steven Trogdon wrote:
>>
>> *Gentoo*
>>
>> Incremental build 9.1.beta8 -> 9.1.beta9
>>
>> After make python3-clean && make I have the following failures:
>>
>> --
>> sage -t --long --warn-long 115.0 src/sage/doctest/test.py  # 1 doctest 
>> failed
>> sage -t --long --warn-long 115.0 src/sage/rings/integer.pyx  # 2 doctests 
>> failed
>> --
>>
>> System python is 3.7.6
>>
>> The failures:
>>
>> sage -t --long --warn-long 115.0 src/sage/doctest/test.py
>> **
>> File "src/sage/doctest/test.py", line 521, in sage.doctest.test
>> Failed example:
>> if system() == "Linux":
>> P = subprocess.Popen(["sage", "-t", "--warn-long", "0", 
>> "--memlimit=2000", "memlimit.rst"], stdout=subprocess.PIPE, **kwds)
>> out, err = P.communicate()
>> ok = ("MemoryError: failed to allocate" in bytes_to_str(out))
>> Expected nothing
>> Got:
>> Process DocTestWorker-1:
>> Traceback (most recent call last):
>>   File "/usr/lib/python3.7/multiprocessing/process.py", line 297, in 
>> _bootstrap
>> self.run()
>>   File 
>> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>  
>> line 2172, in run
>> task(self.options, self.outtmpfile, msgpipe, self.result_queue)
>>   File 
>> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>  
>> line 2525, in __call__
>> result_queue.put(result, False)
>>   File "/usr/lib/python3.7/multiprocessing/queues.py", line 87, in put
>> self._start_thread()
>>   File "/usr/lib/python3.7/multiprocessing/queues.py", line 170, in 
>> _start_thread
>> self._thread.start()
>>   File "/usr/lib/python3.7/threading.py", line 852, in start
>> _start_new_thread(self._bootstrap, ())
>> RuntimeError: can't start new thread
>> **
>>
>> sage -t --long --warn-long 115.0 src/sage/rings/integer.pyx
>> **
>> File "src/sage/rings/integer.pyx", line 3118, in 
>> sage.rings.integer.Integer.divisors
>> Failed example:
>> for i in range(20):  # long time
>> try:
>> alarm(RDF.random_element(1e-3, 0.5))
>> _ = n.divisors()
>> cancel_alarm()  # we never get here
>> except AlarmInterrupt:
>> pass
>> Exception raised:
>> Traceback (most recent call last):
>>   File 
>> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>  
>> line 681, in _run
>> self.compile_and_execute(example, compiler, test.globs)
>>   File 
>> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>  
>> line 1123, in compile_and_execute
>> exec(compiled, globs)
>>   File "", line 4, 
>> in 
>> _ = n.divisors()
>>   File "sage/rings/integer.pyx", line 3188, in 
>> sage.rings.integer.Integer.divisors 
>> (build/cythonized/sage/rings/integer.c:20544)
>> ptr = check_allocarray(divisor_count, 3 * 
>> sizeof(unsigned long))
>>   File "memory.pxd", line 87, in cysignals.memory.check_allocarray 
>> (build/cythonized/sage/rings/integer.c:46769)
>> MemoryError: failed to allocate 33554432 * 24 bytes
>> **
>> File "src/sage/rings/integer.pyx", line 3790, in 
>> sage.rings.integer.Integer.trial_division
>> Failed example:
>> n = 2 * next_prime(10^40); n.trial_division()
>> Exception raised:
>> Traceback (most recent call last):
>>   File 
>> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>  
>> line 681, in _run
>> self.compile_and_execute(example, compiler, test.globs)
>>   File 
>> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>>  
>> line 1123, in compile_and_

[sage-release] Re: Sage 9.1.beta9 released

[Sébastien Labbé]

Testing with many optional and external packages, I get

Using 
--optional=4ti2,cbc,ccache,cryptominisat,dot2tex,e_antic,external,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_numerical_backends_cplex,sage_numerical_backends_gurobi

--
sage -t --long src/sage/databases/findstat.py  # 8 doctests failed
sage -t --long src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Bad exit: 14
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests 
failed
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
sage -t --long src/sage/symbolic/integration/external.py  # 1 doctest failed
--
External software detected for doctesting: 
cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

Rerunning failed tests, I get:

--
sage -t --long src/sage/databases/findstat.py  # 8 doctests failed
sage -t --long src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Bad exit: 1
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests 
failed
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
--
External software detected for doctesting: ffmpeg,imagemagick,internet

These are known issues. Follow up at https://trac.sagemath.org/ticket/25536

The external.py failing test which does not reproduce is copied below.

sage -t --long src/sage/symbolic/integration/external.py
**
File "src/sage/symbolic/integration/external.py", line 91, in 
sage.symbolic.integration.external.mma_free_integrator
Failed example:
integral(sin(y)^2, y, algorithm='mathematica_free') # optional - 
internet
Expected:
1/2*y - 1/4*sin(2*y)
Got:
-1/2*cos(y)*sin(y) + 1/2*y
**
1 item had failures:
   1 of   7 in sage.symbolic.integration.external.mma_free_integrator
8 fricas tests not run
0 tests not run because we ran out of time
[36 tests, 1 failure, 21.85 s]

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[sage-release] Re: Sage 9.1.beta9 released

[Steven Trogdon]

I'm replying to my previous post.

I rebuilt Sage using the Sage-provided python instead my system python and 
doctested Sage. The failure in doctest/test.py disappears. However, the 
failures in rings/integer.pyx still persist. I suspect a system component 
is the culprit. Any ideas which one? I had doctested 9.1.beta8 with no 
failures, so something has changed.

On Monday, March 30, 2020 at 4:54:19 PM UTC-5, Steven Trogdon wrote:
>
> *Gentoo*
>
> Incremental build 9.1.beta8 -> 9.1.beta9
>
> After make python3-clean && make I have the following failures:
>
> --
> sage -t --long --warn-long 115.0 src/sage/doctest/test.py  # 1 doctest 
> failed
> sage -t --long --warn-long 115.0 src/sage/rings/integer.pyx  # 2 doctests 
> failed
> --
>
> System python is 3.7.6
>
> The failures:
>
> sage -t --long --warn-long 115.0 src/sage/doctest/test.py
> **
> File "src/sage/doctest/test.py", line 521, in sage.doctest.test
> Failed example:
> if system() == "Linux":
> P = subprocess.Popen(["sage", "-t", "--warn-long", "0", 
> "--memlimit=2000", "memlimit.rst"], stdout=subprocess.PIPE, **kwds)
> out, err = P.communicate()
> ok = ("MemoryError: failed to allocate" in bytes_to_str(out))
> Expected nothing
> Got:
> Process DocTestWorker-1:
> Traceback (most recent call last):
>   File "/usr/lib/python3.7/multiprocessing/process.py", line 297, in 
> _bootstrap
> self.run()
>   File 
> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>  
> line 2172, in run
> task(self.options, self.outtmpfile, msgpipe, self.result_queue)
>   File 
> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>  
> line 2525, in __call__
> result_queue.put(result, False)
>   File "/usr/lib/python3.7/multiprocessing/queues.py", line 87, in put
> self._start_thread()
>   File "/usr/lib/python3.7/multiprocessing/queues.py", line 170, in 
> _start_thread
> self._thread.start()
>   File "/usr/lib/python3.7/threading.py", line 852, in start
> _start_new_thread(self._bootstrap, ())
> RuntimeError: can't start new thread
> **
>
> sage -t --long --warn-long 115.0 src/sage/rings/integer.pyx
> **
> File "src/sage/rings/integer.pyx", line 3118, in 
> sage.rings.integer.Integer.divisors
> Failed example:
> for i in range(20):  # long time
> try:
> alarm(RDF.random_element(1e-3, 0.5))
> _ = n.divisors()
> cancel_alarm()  # we never get here
> except AlarmInterrupt:
> pass
> Exception raised:
> Traceback (most recent call last):
>   File 
> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>  
> line 681, in _run
> self.compile_and_execute(example, compiler, test.globs)
>   File 
> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>  
> line 1123, in compile_and_execute
> exec(compiled, globs)
>   File "", line 4, in 
> 
> _ = n.divisors()
>   File "sage/rings/integer.pyx", line 3188, in 
> sage.rings.integer.Integer.divisors 
> (build/cythonized/sage/rings/integer.c:20544)
> ptr = check_allocarray(divisor_count, 3 * 
> sizeof(unsigned long))
>   File "memory.pxd", line 87, in cysignals.memory.check_allocarray 
> (build/cythonized/sage/rings/integer.c:46769)
> MemoryError: failed to allocate 33554432 * 24 bytes
> **
> File "src/sage/rings/integer.pyx", line 3790, in 
> sage.rings.integer.Integer.trial_division
> Failed example:
> n = 2 * next_prime(10^40); n.trial_division()
> Exception raised:
> Traceback (most recent call last):
>   File 
> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>  
> line 681, in _run
> self.compile_and_execute(example, compiler, test.globs)
>   File 
> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
>  
> line 1123, in compile_and_execute
> exec(compiled, globs)
>   File "", line 
> 1, in 
> n = Integer(2) * next_prime(Integer(10)**Integer(40)); 
> n.trial_division()
>   File 
> "/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/arith/misc.py",
>  
> line 1193, in next_prime
> return ZZ(n).next_prime(proof)
>   File "sage/rings/integer.pyx", line 5774, in 
> sage.rings.integer.Integer.next_prime 
> (bui

Re: [sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 3:03:14 PM UTC-4, vdelecroix wrote:
>
>
> Le 29/03/2020 à 21:50, Matthias Köppe a écrit : 
> > 
> > Let me remark that this is the first beta that tries to use the system 
> > python3 in a venv (#27824) instead of building our own copy of python3. 
> > Tests of building from scratch or (after "make python3-clean") would be 
> > valuable. 
>
> Very disappointing 
>
> configure:25182: checking ... whether /usr/bin/python3 is good 
> configure:25329: result: no, Python 3.8.2 is too recent 
>
>
You can override this by:
./configure PYTHON3=/usr/bin/python3

but then you will likely run into the issues discussed on the Python 3.8 
upgrade ticket (https://trac.sagemath.org/ticket/27754).

Matthias

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Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

On Tue, Mar 31, 2020 at 9:35 PM Steven Trogdon  wrote:
>
> A feature or a bug? 'make distclean && make' always uses the system python to 
> build Sage. Is there some way to force building and using the Sage-supplied 
> python?

sure, you can use ./configure -h to see how to have packages built
Namely

./configure --with-system-python3=no

will do this for you.

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[sage-release] Re: Sage 9.1.beta9 released

[Steven Trogdon]

A feature or a bug? 'make distclean && make' always uses the system python 
to build Sage. Is there some way to force building and using the 
Sage-supplied python?

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Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

On Tue, Mar 31, 2020 at 7:46 PM Simon King  wrote:
>
> Hi all,
>
> On 2020-03-31, Matthias Köppe  wrote:
> >> > I don't know, but I found these instructions:
> >> > https://launchpad.net/~deadsnakes/+archive/ubuntu/ppa
> >> > that also mention what packages should be installed
> >>
> >> Excellent! After installing them and doing ./configure, I see this line:
> >>  python3-3.7.3.p1:using system package; SPKG
> >> will not be installed
> >>
> >>
> > Great, this looks like progress. And thanks for telling me about the
> > deadsnakes ppa, this may be useful at some point.
> >
> >
> >> So, now I can try whether it works
> >>
> >>
> > If it doesn't, please post the logs, as usual.
>
> It *almost* worked. On Ubuntu 16.04 with Python 3.7.7 installed from a
> ppa, I get
> sage -t --warn-long 44.6 src/sage/rings/padics/padic_lattice_element.py  # 3 
> doctests failed

this is a well-known bug/feature - the authors of this code have hard
time deciding whether
this should remain experimental, or not...
(I don't understand why on some platforms these tests fail, while on
some they don't)
https://trac.sagemath.org/ticket/29272



> sage -t --warn-long 44.6 src/sage/interfaces/psage.py  # 1 doctest failed
>
> with SageMath version 9.1.beta9, Release Date: 2020-03-29.
>
> I posted config.log, dochtml.doc, install.log, start.log and test.log
> here: https://users.fmi.uni-jena.de/~king/logs/
>
> Best regards,
> Simon
>
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[sage-release] Re: Sage 9.1.beta9 released

[Simon King]

Hi all,

On 2020-03-31, Matthias Köppe  wrote:
>> > I don't know, but I found these instructions: 
>> > https://launchpad.net/~deadsnakes/+archive/ubuntu/ppa 
>> > that also mention what packages should be installed 
>>
>> Excellent! After installing them and doing ./configure, I see this line: 
>>  python3-3.7.3.p1:using system package; SPKG 
>> will not be installed 
>>
>>
> Great, this looks like progress. And thanks for telling me about the 
> deadsnakes ppa, this may be useful at some point.
>  
>
>> So, now I can try whether it works
>>
>>
> If it doesn't, please post the logs, as usual.

It *almost* worked. On Ubuntu 16.04 with Python 3.7.7 installed from a
ppa, I get
sage -t --warn-long 44.6 src/sage/rings/padics/padic_lattice_element.py  # 3 
doctests failed
sage -t --warn-long 44.6 src/sage/interfaces/psage.py  # 1 doctest failed

with SageMath version 9.1.beta9, Release Date: 2020-03-29.

I posted config.log, dochtml.doc, install.log, start.log and test.log
here: https://users.fmi.uni-jena.de/~king/logs/

Best regards,
Simon

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 8:59:06 PM UTC-4, Simon King wrote:
>
> On 2020-03-31, Matthias Köppe > wrote: 
> > On Monday, March 30, 2020 at 8:30:34 PM UTC-4, Simon King wrote: 
> >> 
> >> I installed python3 after "sudo add-apt-repository ppa:deadsnakes/ppa". 
> >> Has that been a mistake? 
> >> 
> >> 
> > I don't know, but I found these instructions: 
> > https://launchpad.net/~deadsnakes/+archive/ubuntu/ppa 
> > that also mention what packages should be installed 
>
> Excellent! After installing them and doing ./configure, I see this line: 
>  python3-3.7.3.p1:using system package; SPKG 
> will not be installed 
>
>
Great, this looks like progress. And thanks for telling me about the 
deadsnakes ppa, this may be useful at some point.
 

> So, now I can try whether it works
>
>
If it doesn't, please post the logs, as usual.

Best,
Matthias
 

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[sage-release] Re: Sage 9.1.beta9 released

[Simon King]

Dear Matthias,

On 2020-03-31, Matthias Köppe  wrote:
> On Monday, March 30, 2020 at 8:30:34 PM UTC-4, Simon King wrote:
>>
>> > Are you sure your /usr/bin/python comes from that distribution? As far 
>> as I 
>> > can see, xenial only has 3.5.1-3. 
>>
>> I installed python3 after "sudo add-apt-repository ppa:deadsnakes/ppa". 
>> Has that been a mistake? 
>>
>>
> I don't know, but I found these instructions: 
> https://launchpad.net/~deadsnakes/+archive/ubuntu/ppa
> that also mention what packages should be installed

Excellent! After installing them and doing ./configure, I see this line:
 python3-3.7.3.p1:using system package; SPKG will 
not be installed

So, now I can try whether it works (and of course if it doesn't I can
still try sudo apt-get remove python3.7 and change the symlinks
/usr/bin/python and /usr/bin/python3 to my distribution's standard
python3.5).

Thank you for your help!
Best regards,
Simon

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 8:30:34 PM UTC-4, Simon King wrote:
>
> > Are you sure your /usr/bin/python comes from that distribution? As far 
> as I 
> > can see, xenial only has 3.5.1-3. 
>
> I installed python3 after "sudo add-apt-repository ppa:deadsnakes/ppa". 
> Has that been a mistake? 
>
>
I don't know, but I found these instructions: 
https://launchpad.net/~deadsnakes/+archive/ubuntu/ppa
that also mention what packages should be installed
 

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[sage-release] Re: Sage 9.1.beta9 released

[Simon King]

On 2020-03-30, Matthias Köppe  wrote:
> Hi Simon,
>
> On Monday, March 30, 2020 at 6:45:17 PM UTC-4, Simon King wrote:
>> Concerning too old: 
>> $ uname -a 
>> Linux klap 4.15.0-91-generic #92~16.04.1-Ubuntu SMP Fri Feb 28 14:57:22 
>> UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 
>> $ cat /etc/issue 
>> Ubuntu 16.04.6 LTS \n \l 
>>
>> I posted config.log here: https://users.fmi.uni-jena.de/~king/config.log 
>>
>>
> Are you sure your /usr/bin/python comes from that distribution? As far as I 
> can see, xenial only has 3.5.1-3.

I installed python3 after "sudo add-apt-repository ppa:deadsnakes/ppa".
Has that been a mistake? How to undo it?

Best regards,
Simon

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 6:59:30 PM UTC-4, John H Palmieri wrote:
>
> I see the same in the log file for the Python 2 build. I wonder if this 
> has to do with upgrading Xcode, which I seem to have done 6 days ago. To be 
> clear, yesterday and today I have built  9.1.beta8 + Python 3 and 9.1.beta9 
> + Python 2, both successfully, despite this crash. It's 9.1.beta9 + Python 
> 3 which is causing problems. It also seems to be using the Apple Python 3, 
> /usr/bin/python3, not the one installed by homebrew.
>

I'll try upgrading XCode to try to reproduce these errors. (My gcc reports 
"Apple clang version 11.0.0 (clang-1100.0.33.17) Target: 
x86_64-apple-darwin19.3.0").

FWIW, I just ran "tox -e local-macos-homebrew-standard -- build ptest" 
(as of https://trac.sagemath.org/ticket/29417 it uses the python3 from 
homebrew)
and it completed with only 1 doctest error in src/sage/interfaces/gap.py.

Did you follow homebrew's instructions regarding the "keg-only packages"? 
For example, readline is only installed in /usr/local/opt/readline, not in 
/usr/local.

Sage now has a helper shell script that you can source to set up the 
environment for those. 
Try ". .homebrew-build-env " before running configure.


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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 7:16:26 PM UTC-4, Matthias Köppe wrote:
>
> Hi Simon,
>
> On Monday, March 30, 2020 at 6:45:17 PM UTC-4, Simon King wrote:
>>
>> Trying what src/doc/en/installation/debian*.txt tells me: 
>> Note, selecting 'zlib1g-dev' instead of 'libz-dev' 
>> E: Unable to locate package libflint-arb-dev 
>> E: Unable to locate package libplanarity-dev 
>> E: Unable to locate package python3-distutils 
>>
>
> That looks as expected for Ubuntu 16.04 (xenial).
>  
>
>> Concerning too old: 
>> $ uname -a 
>> Linux klap 4.15.0-91-generic #92~16.04.1-Ubuntu SMP Fri Feb 28 14:57:22 
>> UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 
>> $ cat /etc/issue 
>> Ubuntu 16.04.6 LTS \n \l 
>>
>> I posted config.log here: https://users.fmi.uni-jena.de/~king/config.log 
>>
>>
> Are you sure your /usr/bin/python comes from that distribution? As far as 
> I can see, xenial only has 3.5.1-3.
>
>
I meant /usr/bin/python3.7, not /usr/bin/python.



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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

Hi Simon,

On Monday, March 30, 2020 at 6:45:17 PM UTC-4, Simon King wrote:
>
> Trying what src/doc/en/installation/debian*.txt tells me: 
> Note, selecting 'zlib1g-dev' instead of 'libz-dev' 
> E: Unable to locate package libflint-arb-dev 
> E: Unable to locate package libplanarity-dev 
> E: Unable to locate package python3-distutils 
>

That looks as expected for Ubuntu 16.04 (xenial).
 

> Concerning too old: 
> $ uname -a 
> Linux klap 4.15.0-91-generic #92~16.04.1-Ubuntu SMP Fri Feb 28 14:57:22 
> UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 
> $ cat /etc/issue 
> Ubuntu 16.04.6 LTS \n \l 
>
> I posted config.log here: https://users.fmi.uni-jena.de/~king/config.log 
>
>
Are you sure your /usr/bin/python comes from that distribution? As far as I 
can see, xenial only has 3.5.1-3.



 

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[sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

I see the same in the log file for the Python 2 build. I wonder if this has 
to do with upgrading Xcode, which I seem to have done 6 days ago. To be 
clear, yesterday and today I have built  9.1.beta8 + Python 3 and 9.1.beta9 
+ Python 2, both successfully, despite this crash. It's 9.1.beta9 + Python 
3 which is causing problems. It also seems to be using the Apple Python 3, 
/usr/bin/python3, not the one installed by homebrew.

For what it's worth:

- I don't see this crash message from config.log files from a few weeks ago.
- the message refers to a file 

/Users/palmieri/Library/Logs/DiagnosticReports/clang__.crash,

but there is no such file.



On Monday, March 30, 2020 at 1:44:41 PM UTC-7, Matthias Köppe wrote:
>
> From your config.log ... rather suspicious:
>
> configure:10189: g++ -std=gnu++11 -o conftest -g -O2   conftest.cpp -lgmp  
> -lm  >&5
> configure:10189: $? = 0
> configure:10206: result: -lgmp
> configure:10231: will use system package and not install SPKG mpir
> configure:10265: checking absolute name of 
> configure:10272: checking for gmp.h
> configure:10272: result: yes
> clang: error: unable to execute command: Broken pipe: 13
> clang: error: clang frontend command failed due to signal (use -v to see 
> invocation)
> Apple clang version 11.0.3 (clang-1103.0.32.29)
> Target: x86_64-apple-darwin19.3.0
> Thread model: posix
> InstalledDir: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
> clang: note: diagnostic msg: PLEASE submit a bug report to 
> http://developer.apple.com/bugreporter/ and include the crash backtrace, 
> preprocessed source, and associated run script.
> clang: note: diagnostic msg: 
> 
>
> PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
> Preprocessed source(s) and associated run script(s) are located at:
> clang: note: diagnostic msg: 
> /var/folders/cp/n8wtqs490tq5psknff1hv9qrgn/T/conftest-d428b4.cpp
> clang: note: diagnostic msg: 
> /var/folders/cp/n8wtqs490tq5psknff1hv9qrgn/T/conftest-d428b4.sh
> clang: note: diagnostic msg: Crash backtrace is located in
> clang: note: diagnostic msg: 
> /Users/palmieri/Library/Logs/DiagnosticReports/clang__.crash
> clang: note: diagnostic msg: (choose the .crash file that corresponds to your 
> crash)
> clang: note: diagnostic msg: 
>
> 
> configure:10296: result: ///usr/local/include/gmp.h
> configure:10332: result: using GMP-compatible library from the system
> ##  ##
> ## Checking whether SageMath should install SPKG gmp... ##
> ##  ##
> configure:10415: will use system package and not install SPKG gmp
>
>
>
> This seems to come from AX_ABSOLUTE_HEADER 
>
>
>
> On Monday, March 30, 2020 at 12:18:41 PM UTC-4, John H Palmieri wrote:
>>
>>
>> config.log attached.
>>
>

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[sage-release] Re: Sage 9.1.beta9 released

[Simon King]

Hi Matthias,

On 2020-03-30, Matthias Köppe  wrote:
> This is outdated. We now generate an up-to-date version of this manual 
> section at boostrapping time. Use "cat src/doc/en/installation/debian*.txt" 
> to print it.
>
> Or re-run configure and take a look at the system package installation 
> hints that it prints at the very end.
>
> (but note that libflint-arb-dev isn't available for me in ubuntu, no 
>> idea why), 
>
>
> Likely your ubuntu is too old.

Thanks. Trying what src/doc/en/installation/debian*.txt tells me:
Note, selecting 'zlib1g-dev' instead of 'libz-dev'
E: Unable to locate package libflint-arb-dev
E: Unable to locate package libplanarity-dev
E: Unable to locate package python3-distutils

Concerning too old:
$ uname -a
Linux klap 4.15.0-91-generic #92~16.04.1-Ubuntu SMP Fri Feb 28 14:57:22 UTC 
2020 x86_64 x86_64 x86_64 GNU/Linux
$ cat /etc/issue
Ubuntu 16.04.6 LTS \n \l

I posted config.log here: https://users.fmi.uni-jena.de/~king/config.log

Best regards,
Simon

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 5:54:19 PM UTC-4, Steven Trogdon wrote:
>
> *Gentoo [...]*
>
>>
>>
Please help with https://trac.sagemath.org/ticket/29105 so that builds on 
top of Gentoo can be properly tested.


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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

Hi Simon,

On Monday, March 30, 2020 at 6:20:24 PM UTC-4, Simon King wrote:
>
> Let me add further disappointments: 
>
> After making sure that python3.7.7 is installed on my laptop and after 
> installing the recommended system packages mentioned in 
>
> http://doc.sagemath.org/html/en/installation/source.html#linux-recommended-installation
>  
>

This is outdated. We now generate an up-to-date version of this manual 
section at boostrapping time. Use "cat src/doc/en/installation/debian*.txt" 
to print it.

Or re-run configure and take a look at the system package installation 
hints that it prints at the very end.

(but note that libflint-arb-dev isn't available for me in ubuntu, no 
> idea why), 


Likely your ubuntu is too old.
 
> configure:25066: checking ... whether /usr/bin/python3.7 is good 
> configure:25200: result: no, the version is in the supported range, and 
the modules can be imported, but distutils cannot build an extension 

Post config.log, and we can take a closer look.



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[sage-release] Re: Sage 9.1.beta9 released

[Simon King]

Hi!

On 2020-03-30, Dima Pasechnik  wrote:
> On Tue, 31 Mar 2020, 03:03 Vincent Delecroix, <20100.delecr...@gmail.com>
> wrote:
>> Le 29/03/2020 à 21:50, Matthias Köppe a écrit :
>> >
>> > Let me remark that this is the first beta that tries to use the system
>> > python3 in a venv (#27824) instead of building our own copy of python3.
>> > Tests of building from scratch or (after "make python3-clean") would be
>> > valuable.
>>
>> Very disappointing

Let me add further disappointments:

After making sure that python3.7.7 is installed on my laptop and after
installing the recommended system packages mentioned in
http://doc.sagemath.org/html/en/installation/source.html#linux-recommended-installation
(but note that libflint-arb-dev isn't available for me in ubuntu, no
idea why), I get this in my config.log:

## Checking whether SageMath should install SPKG python3... ##
##  ##
configure:25026: checking whether any of sqlite libpng bzip2 xz libffi is 
installed or will be installed as SPKG
configure:25030: result: yes; install python3 as well
configure:25273: no suitable system package found for SPKG python3

Concerning sqlite, I see this:
## Checking whether SageMath should install SPKG sqlite... ##
## --- ##
configure:24630: checking libsqlite3 >= sqlite3_min_version
configure:24664: g++ -std=gnu++11 -o conftest -g -O2conftest.cpp -lm4rie 
-lgf2x -lreadline -L/usr/lib/x86_64-linux-gnu -lcurl -lbz2 -lgmp -lm  -lntl 
-lsqlite3 >&5
conftest.cpp:69:62: fatal error: sqlite3.h: No such file or directory

So, apparently libsqlite3-dev needs to be installed (it isn't mentioned in the
list of recommended packages), the other stuff (libpng, bzip2, xz,
libffi apparently is installed on my system).

After installing libsqlite3-dev, I get another problem:
##  ##
## Checking whether SageMath should install SPKG python3... ##
##  ##
configure:25026: checking whether any of sqlite libpng bzip2 xz libffi is 
installed or will be installed as SPKG
configure:25035: result: no
configure:25045: checking for python3 >= 3.7.3, < 3.8 with modules sqlite3, 
ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:25051: result: 
configure:25066: checking ... whether /usr/bin/python3.7 is good
configure:25200: result: no, the version is in the supported range, and the 
modules can be imported, but distutils cannot build an extension
configure:25066: checking ... whether /usr/bin/python3 is good
configure:25200: result: no, the version is in the supported range, and the 
modules can be imported, but distutils cannot build an extension
configure:25247: result: 
configure:25273: no suitable system package found for SPKG python3

Since it mentions "extensions", I was trying to install cython3. But
this didn't help, distutils still cannot build an extension. So, I tried
to install python3-distutils (but this is not available in ubuntu) and
eventually python3-distutils-extra.

Result:
Still doesn't work.

So, it seems to be that the following updates to the Sage installation
guide should be done:

- Something should be done about libflint-arb-dev
- libsqlite3-dev should be added
- It should be explained what to do concerning the system python3's
  distutils' inability to build extensions.

Best regards,
Simon

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[sage-release] Re: Sage 9.1.beta9 released

[Steven Trogdon]

*Gentoo*

Incremental build 9.1.beta8 -> 9.1.beta9

After make python3-clean && make I have the following failures:

--
sage -t --long --warn-long 115.0 src/sage/doctest/test.py  # 1 doctest 
failed
sage -t --long --warn-long 115.0 src/sage/rings/integer.pyx  # 2 doctests 
failed
--

System python is 3.7.6

The failures:

sage -t --long --warn-long 115.0 src/sage/doctest/test.py
**
File "src/sage/doctest/test.py", line 521, in sage.doctest.test
Failed example:
if system() == "Linux":
P = subprocess.Popen(["sage", "-t", "--warn-long", "0", 
"--memlimit=2000", "memlimit.rst"], stdout=subprocess.PIPE, **kwds)
out, err = P.communicate()
ok = ("MemoryError: failed to allocate" in bytes_to_str(out))
Expected nothing
Got:
Process DocTestWorker-1:
Traceback (most recent call last):
  File "/usr/lib/python3.7/multiprocessing/process.py", line 297, in 
_bootstrap
self.run()
  File 
"/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 2172, in run
task(self.options, self.outtmpfile, msgpipe, self.result_queue)
  File 
"/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 2525, in __call__
result_queue.put(result, False)
  File "/usr/lib/python3.7/multiprocessing/queues.py", line 87, in put
self._start_thread()
  File "/usr/lib/python3.7/multiprocessing/queues.py", line 170, in 
_start_thread
self._thread.start()
  File "/usr/lib/python3.7/threading.py", line 852, in start
_start_new_thread(self._bootstrap, ())
RuntimeError: can't start new thread
**

sage -t --long --warn-long 115.0 src/sage/rings/integer.pyx
**
File "src/sage/rings/integer.pyx", line 3118, in 
sage.rings.integer.Integer.divisors
Failed example:
for i in range(20):  # long time
try:
alarm(RDF.random_element(1e-3, 0.5))
_ = n.divisors()
cancel_alarm()  # we never get here
except AlarmInterrupt:
pass
Exception raised:
Traceback (most recent call last):
  File 
"/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 681, in _run
self.compile_and_execute(example, compiler, test.globs)
  File 
"/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 1123, in compile_and_execute
exec(compiled, globs)
  File "", line 4, in 

_ = n.divisors()
  File "sage/rings/integer.pyx", line 3188, in 
sage.rings.integer.Integer.divisors 
(build/cythonized/sage/rings/integer.c:20544)
ptr = check_allocarray(divisor_count, 3 * 
sizeof(unsigned long))
  File "memory.pxd", line 87, in cysignals.memory.check_allocarray 
(build/cythonized/sage/rings/integer.c:46769)
MemoryError: failed to allocate 33554432 * 24 bytes
**
File "src/sage/rings/integer.pyx", line 3790, in 
sage.rings.integer.Integer.trial_division
Failed example:
n = 2 * next_prime(10^40); n.trial_division()
Exception raised:
Traceback (most recent call last):
  File 
"/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 681, in _run
self.compile_and_execute(example, compiler, test.globs)
  File 
"/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/doctest/forker.py",
 
line 1123, in compile_and_execute
exec(compiled, globs)
  File "", line 
1, in 
n = Integer(2) * next_prime(Integer(10)**Integer(40)); 
n.trial_division()
  File 
"/mnt/backup/storage/sage-git_develop/sage/local/lib/python3.7/site-packages/sage/arith/misc.py",
 
line 1193, in next_prime
return ZZ(n).next_prime(proof)
  File "sage/rings/integer.pyx", line 5774, in 
sage.rings.integer.Integer.next_prime 
(build/cythonized/sage/rings/integer.c:35865)
while not p._pseudoprime_is_prime(proof):
  File "sage/rings/integer.pyx", line 5309, in 
sage.rings.integer.Integer._pseudoprime_is_prime 
(build/cythonized/sage/rings/integer.c:33383)
return self.__pari__().isprime()
  File "cypari2/gen.pyx", line 2112, in cypari2.gen.Gen.isprime
cysignals.signals.AlarmInterrupt
**
2 items had failures:
   1 of  23 in sage.rings.integer.Integer.divisors
   1 of  19 in sage.rings.integer.Integer.trial_division


On Sunday, March 29, 2020 at 2:50:19 PM UTC-5, Matthias Köppe wrote:
>
> On S

[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

>From your config.log ... rather suspicious:

configure:10189: g++ -std=gnu++11 -o conftest -g -O2   conftest.cpp -lgmp  -lm  
>&5
configure:10189: $? = 0
configure:10206: result: -lgmp
configure:10231: will use system package and not install SPKG mpir
configure:10265: checking absolute name of 
configure:10272: checking for gmp.h
configure:10272: result: yes
clang: error: unable to execute command: Broken pipe: 13
clang: error: clang frontend command failed due to signal (use -v to see 
invocation)
Apple clang version 11.0.3 (clang-1103.0.32.29)
Target: x86_64-apple-darwin19.3.0
Thread model: posix
InstalledDir: 
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
clang: note: diagnostic msg: PLEASE submit a bug report to 
http://developer.apple.com/bugreporter/ and include the crash backtrace, 
preprocessed source, and associated run script.
clang: note: diagnostic msg: 


PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: 
/var/folders/cp/n8wtqs490tq5psknff1hv9qrgn/T/conftest-d428b4.cpp
clang: note: diagnostic msg: 
/var/folders/cp/n8wtqs490tq5psknff1hv9qrgn/T/conftest-d428b4.sh
clang: note: diagnostic msg: Crash backtrace is located in
clang: note: diagnostic msg: 
/Users/palmieri/Library/Logs/DiagnosticReports/clang__.crash
clang: note: diagnostic msg: (choose the .crash file that corresponds to your 
crash)
clang: note: diagnostic msg: 


configure:10296: result: ///usr/local/include/gmp.h
configure:10332: result: using GMP-compatible library from the system
##  ##
## Checking whether SageMath should install SPKG gmp... ##
##  ##
configure:10415: will use system package and not install SPKG gmp



This seems to come from AX_ABSOLUTE_HEADER 



On Monday, March 30, 2020 at 12:18:41 PM UTC-4, John H Palmieri wrote:
>
>
> config.log attached.
>

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Re: [sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

I ran "brew upgrade" and it only upgraded a few packages: tox, cmake, 
boost, automake, and some port of emacs. I rebuilt Sage and it didn't help. 
(Just to be sure, I also built 9.1.beta8, and that one passes tests.)


On Monday, March 30, 2020 at 9:30:26 AM UTC-7, Dima Pasechnik wrote:
>
> I vaguely recall seeing similar errors on Homebrew, they were due to 
> stale Homebrew. Could you try updating it? 
>
> On Tue, Mar 31, 2020 at 12:23 AM John H Palmieri  > wrote: 
> > 
> > I should also mention that I have built every beta from scratch for 
> Python 2 and 3 for quite a while, and these failures are new. So if the gcc 
> in homebrew is getting picked up, it's because of some new change in Sage. 
> > 
> > 
> > On Sunday, March 29, 2020 at 10:01:31 PM UTC-7, Dima Pasechnik wrote: 
> >> 
> >> Could it be that gcc in Homebrew gets picked to compile C/C++ code? 
> >> 
> >> On Mon, Mar 30, 2020 at 12:36 PM John H Palmieri  
> wrote: 
> >> > 
> >> > On OS X with a homebrew installation of Python 3.7.7 I get some 
> failures, mostly to do with pari, including messages like this: 
> >> > 
> >> > PARI/GP ERROR: 
> >> >   ***   bug in PARI/GP (Segmentation Fault), please report. 
> >> > 
> >> > 
> >> > and this: 
> >> > 
> >> > fatal error: 'gmp.h' file not found 
> >> > #include "gmp.h" 
> >> >  ^~~ 
> >> > 1 error generated. 
> >> > 
> >> > and this: 
> >> > 
> >> > RuntimeError: command 'gcc' failed with exit status 1 
> >> > ld: library not found for -lmpfr 
> >> > clang: error: linker command failed with exit code 1 (use -v to see 
> invocation) 
> >> > 
> >> > "System" packages being used, according to config.log: 
> >> > 
> >> > boost, boost_cropped, bzip2, cmake, curl, freetype, gcc, gfortran, 
> git, gmp, iconv, isl, libffi, libgd, libpng, mpc, mpfi, mpfr, mpir, 
> ncurses, ninja_build, patch, pcre,pkgconf, python, sqlite, xz, yasm, 
> zeromq, zlib 
> >> > 
> >> > gsl, openblas, r, and readline are also installed via homebrew, but 
> ./configure doesn't seem to like them. 
> >> > 
> >> > Failures: 
> >> > 
> >> > 
> -- 
> >> > sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_number_field.py  # 19 doctests failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_rational_field.py  # 31 doctests 
> failed 
> >> > sage -t --long --warn-long 72.2 src/sage/misc/sagedoc.py  # 2 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/doctest/sources.py  # 1 
> doctest failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/height.py  # 6 doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/symbolic/expression.pyx  # 1 
> doctest failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py
>  
>  # 9 doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/tests/cmdline.py  # 7 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/modular/modform/element.py 
>  # 44 doctests failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/rings/number_field/number_field.py  # 2 doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/combinat/tableau_tuple.py  # 
> 4 doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/arith/misc.py  # 8 doctests 
> failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/modular/modform_hecketriangle/readme.py  # 20 doctests failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/interfaces/maxima_abstract.py  # 3 doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/modular/abvar/abvar.py  # 1 
> doctest failed 
> >> > sage -t --long --warn-long 72.2 src/sage/structure/element.pyx  # 44 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/modular/abvar/lseries.py  # 
> 11 doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/doctest/forker.py  # 1 
> doctest failed 
> >> > sage -t --long --warn-long 72.2 src/sage/misc/sageinspect.py  # 35 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/calculus/calculus.py  # 4 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/quadratic_forms/genera/genus.py  # 4 doctests failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/geometry/polyhedron/combinatorial_polyhedron/conversions.pyx  # 24 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/graphs/connectivity.pyx  # 2 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/misc/cachefunc.pyx  # 54 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/misc/cython.py  # 19 
> doctests failed 
> >> > sage -t --long --warn-long 72.2 src/sage/plot/line.py  # 2 doctests 
> failed 
> >> > sage -t --long --warn-long 72.2 
> src/sage/modular/modform/constructor.py  # 1 doctest failed 
> >> > sage -t --long --warn-long 72.2 src/sage/misc/randstate.pyx  # 24 
> doctests failed

Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

On Tue, 31 Mar 2020, 03:03 Vincent Delecroix, <20100.delecr...@gmail.com>
wrote:

>
>
> Le 29/03/2020 à 21:50, Matthias Köppe a écrit :
> >
> > Let me remark that this is the first beta that tries to use the system
> > python3 in a venv (#27824) instead of building our own copy of python3.
> > Tests of building from scratch or (after "make python3-clean") would be
> > valuable.
>
> Very disappointing
>
> configure:25182: checking ... whether /usr/bin/python3 is good
> configure:25329: result: no, Python 3.8.2 is too recent
>

this has been open for a while:
https://trac.sagemath.org/ticket/27754

>
> Vincent
>
> --
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> https://groups.google.com/d/msgid/sage-release/68fb2185-903d-1369-f688-3e3e066ff756%40gmail.com
> .
>

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Re: [sage-release] Re: Sage 9.1.beta9 released

[Vincent Delecroix]

Le 29/03/2020 à 21:50, Matthias Köppe a écrit :


Let me remark that this is the first beta that tries to use the system
python3 in a venv (#27824) instead of building our own copy of python3.
Tests of building from scratch or (after "make python3-clean") would be
valuable.


Very disappointing

configure:25182: checking ... whether /usr/bin/python3 is good
configure:25329: result: no, Python 3.8.2 is too recent

Vincent

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Re: [sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 12:23:00 PM UTC-4, John H Palmieri wrote:
>
> I should also mention that I have built every beta from scratch for Python 
> 2 and 3 for quite a while, and these failures are new. So if the gcc in 
> homebrew is getting picked up, it's because of some new change in Sage.
>

There was no change regarding use of gcc, and from the log it's clear the 
XCode's gcc (clang) is used.

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Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

I vaguely recall seeing similar errors on Homebrew, they were due to
stale Homebrew. Could you try updating it?

On Tue, Mar 31, 2020 at 12:23 AM John H Palmieri  wrote:
>
> I should also mention that I have built every beta from scratch for Python 2 
> and 3 for quite a while, and these failures are new. So if the gcc in 
> homebrew is getting picked up, it's because of some new change in Sage.
>
>
> On Sunday, March 29, 2020 at 10:01:31 PM UTC-7, Dima Pasechnik wrote:
>>
>> Could it be that gcc in Homebrew gets picked to compile C/C++ code?
>>
>> On Mon, Mar 30, 2020 at 12:36 PM John H Palmieri  wrote:
>> >
>> > On OS X with a homebrew installation of Python 3.7.7 I get some failures, 
>> > mostly to do with pari, including messages like this:
>> >
>> > PARI/GP ERROR:
>> >   ***   bug in PARI/GP (Segmentation Fault), please report.
>> >
>> >
>> > and this:
>> >
>> > fatal error: 'gmp.h' file not found
>> > #include "gmp.h"
>> >  ^~~
>> > 1 error generated.
>> >
>> > and this:
>> >
>> > RuntimeError: command 'gcc' failed with exit status 1
>> > ld: library not found for -lmpfr
>> > clang: error: linker command failed with exit code 1 (use -v to see 
>> > invocation)
>> >
>> > "System" packages being used, according to config.log:
>> >
>> > boost, boost_cropped, bzip2, cmake, curl, freetype, gcc, gfortran, git, 
>> > gmp, iconv, isl, libffi, libgd, libpng, mpc, mpfi, mpfr, mpir, ncurses, 
>> > ninja_build, patch, pcre,pkgconf, python, sqlite, xz, yasm, zeromq, zlib
>> >
>> > gsl, openblas, r, and readline are also installed via homebrew, but 
>> > ./configure doesn't seem to like them.
>> >
>> > Failures:
>> >
>> > --
>> > sage -t --long --warn-long 72.2 
>> > src/sage/schemes/elliptic_curves/ell_number_field.py  # 19 doctests failed
>> > sage -t --long --warn-long 72.2 
>> > src/sage/schemes/elliptic_curves/ell_rational_field.py  # 31 doctests 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/misc/sagedoc.py  # 2 doctests 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/doctest/sources.py  # 1 doctest 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/height.py 
>> >  # 6 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/symbolic/expression.pyx  # 1 
>> > doctest failed
>> > sage -t --long --warn-long 72.2 
>> > src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py
>> >   # 9 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/tests/cmdline.py  # 7 doctests 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/modular/modform/element.py  # 44 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 
>> > src/sage/rings/number_field/number_field.py  # 2 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/combinat/tableau_tuple.py  # 4 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/arith/misc.py  # 8 doctests failed
>> > sage -t --long --warn-long 72.2 
>> > src/sage/modular/modform_hecketriangle/readme.py  # 20 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/interfaces/maxima_abstract.py  # 
>> > 3 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/modular/abvar/abvar.py  # 1 
>> > doctest failed
>> > sage -t --long --warn-long 72.2 src/sage/structure/element.pyx  # 44 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/modular/abvar/lseries.py  # 11 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/doctest/forker.py  # 1 doctest 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/misc/sageinspect.py  # 35 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/calculus/calculus.py  # 4 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/quadratic_forms/genera/genus.py  
>> > # 4 doctests failed
>> > sage -t --long --warn-long 72.2 
>> > src/sage/geometry/polyhedron/combinatorial_polyhedron/conversions.pyx  # 
>> > 24 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/graphs/connectivity.pyx  # 2 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/misc/cachefunc.pyx  # 54 doctests 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/misc/cython.py  # 19 doctests 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/plot/line.py  # 2 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/modular/modform/constructor.py  # 
>> > 1 doctest failed
>> > sage -t --long --warn-long 72.2 src/sage/misc/randstate.pyx  # 24 doctests 
>> > failed
>> > sage -t --long --warn-long 72.2 src/sage/modules/free_module_element.pyx  
>> > # 3 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/BSD.py  # 
>> > 3 doctests failed
>> > sage -t --long --warn-long 72.2 src/sage/combinat/partition_tuple.py  # 8 
>> > doctests failed
>> > sage -t --long --warn-long 72.2 
>> > src/doc/en/thematic_tutorials/explicit_methods_in_number_theor

Re: [sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

I should also mention that I have built every beta from scratch for Python 
2 and 3 for quite a while, and these failures are new. So if the gcc in 
homebrew is getting picked up, it's because of some new change in Sage.


On Sunday, March 29, 2020 at 10:01:31 PM UTC-7, Dima Pasechnik wrote:
>
> Could it be that gcc in Homebrew gets picked to compile C/C++ code? 
>
> On Mon, Mar 30, 2020 at 12:36 PM John H Palmieri  > wrote: 
> > 
> > On OS X with a homebrew installation of Python 3.7.7 I get some 
> failures, mostly to do with pari, including messages like this: 
> > 
> > PARI/GP ERROR: 
> >   ***   bug in PARI/GP (Segmentation Fault), please report. 
> > 
> > 
> > and this: 
> > 
> > fatal error: 'gmp.h' file not found 
> > #include "gmp.h" 
> >  ^~~ 
> > 1 error generated. 
> > 
> > and this: 
> > 
> > RuntimeError: command 'gcc' failed with exit status 1 
> > ld: library not found for -lmpfr 
> > clang: error: linker command failed with exit code 1 (use -v to see 
> invocation) 
> > 
> > "System" packages being used, according to config.log: 
> > 
> > boost, boost_cropped, bzip2, cmake, curl, freetype, gcc, gfortran, git, 
> gmp, iconv, isl, libffi, libgd, libpng, mpc, mpfi, mpfr, mpir, ncurses, 
> ninja_build, patch, pcre,pkgconf, python, sqlite, xz, yasm, zeromq, zlib 
> > 
> > gsl, openblas, r, and readline are also installed via homebrew, but 
> ./configure doesn't seem to like them. 
> > 
> > Failures: 
> > 
> > -- 
> > sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_number_field.py  # 19 doctests failed 
> > sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_rational_field.py  # 31 doctests 
> failed 
> > sage -t --long --warn-long 72.2 src/sage/misc/sagedoc.py  # 2 doctests 
> failed 
> > sage -t --long --warn-long 72.2 src/sage/doctest/sources.py  # 1 doctest 
> failed 
> > sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/height.py  # 6 doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/symbolic/expression.pyx  # 1 
> doctest failed 
> > sage -t --long --warn-long 72.2 
> src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py
>  
>  # 9 doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/tests/cmdline.py  # 7 doctests 
> failed 
> > sage -t --long --warn-long 72.2 src/sage/modular/modform/element.py  # 
> 44 doctests failed 
> > sage -t --long --warn-long 72.2 
> src/sage/rings/number_field/number_field.py  # 2 doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/combinat/tableau_tuple.py  # 4 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/arith/misc.py  # 8 doctests 
> failed 
> > sage -t --long --warn-long 72.2 
> src/sage/modular/modform_hecketriangle/readme.py  # 20 doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/interfaces/maxima_abstract.py 
>  # 3 doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/modular/abvar/abvar.py  # 1 
> doctest failed 
> > sage -t --long --warn-long 72.2 src/sage/structure/element.pyx  # 44 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/modular/abvar/lseries.py  # 11 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/doctest/forker.py  # 1 doctest 
> failed 
> > sage -t --long --warn-long 72.2 src/sage/misc/sageinspect.py  # 35 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/calculus/calculus.py  # 4 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/quadratic_forms/genera/genus.py 
>  # 4 doctests failed 
> > sage -t --long --warn-long 72.2 
> src/sage/geometry/polyhedron/combinatorial_polyhedron/conversions.pyx  # 24 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/graphs/connectivity.pyx  # 2 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/misc/cachefunc.pyx  # 54 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/misc/cython.py  # 19 doctests 
> failed 
> > sage -t --long --warn-long 72.2 src/sage/plot/line.py  # 2 doctests 
> failed 
> > sage -t --long --warn-long 72.2 src/sage/modular/modform/constructor.py 
>  # 1 doctest failed 
> > sage -t --long --warn-long 72.2 src/sage/misc/randstate.pyx  # 24 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/modules/free_module_element.pyx 
>  # 3 doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/BSD.py 
>  # 3 doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/combinat/partition_tuple.py  # 
> 8 doctests failed 
> > sage -t --long --warn-long 72.2 
> src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/elliptic_curves.rst
>  
>  # 1 doctest failed 
> > sage -t --long --warn-long 72.2 src/sage/repl/ipython_extension.py  # 2 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/interfaces/expect.py  # 3 
> doctests failed 
> > sage -t --long --warn-long 72.2 src/sage/interfa

Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

On Mon, Mar 30, 2020 at 10:14 PM Thierry
 wrote:
>
> On Mon, Mar 30, 2020 at 10:04:46PM +0800, Dima Pasechnik wrote:
> > On Mon, 30 Mar 2020 at 21:47, Thierry 
> > wrote:
> >
> > > Hi,
> > >
> > > On Sun, Mar 29, 2020 at 12:50:18PM -0700, Matthias Köppe wrote:
> > > > On Sunday, March 29, 2020 at 8:59:43 AM UTC-4, Volker Braun wrote:
> > > > >
> > > > > As always, you can get the latest beta version from the "develop" git
> > > > > branch. Alternatively, the self-contained source tarball is at
> > > > > http://www.sagemath.org/download-latest.html
> > > > >
> > > > > I don't see any major issues for 9.1 any more, so we should soon have
> > > the
> > > > > first rc. If you have anything that you thing should go in then now is
> > > the
> > > > > time to finish it up ;-)
> > > > >
> > > > > 6a4580546f (tag: 9.1.beta9, trac/develop) Updated SageMath version to
> > > > > 9.1.beta9
> > > > >
> > > >
> > > >
> > > > Let me remark that this is the first beta that tries to use the system
> > > > python3 in a venv (#27824) instead of building our own copy of python3.
> > > > Tests of building from scratch or (after "make python3-clean") would be
> > > > valuable.
> > >
> > > Do you suggest all of us to make distclean and ptestlong ?
> >
> > in principle distclean should not be needed, but certainly make
> > python3-clean
> > and installing the corresponding “system” packages.
>
> I am on the way to test it, however it seems that numpy, scipy etc are
> not taken into account.
>
at the moment no packages of the system python are used.
cf https://trac.sagemath.org/ticket/29023

> Ciao,
> Thierry
>
>
> > e.g. I don’t think we tested python (should  be python 3.7, i.e. not the
> > latest) from python.org on MacOS.
> >
> > Dima
> >
> >
> > >
> > > Ciao,
> > > Thierry
> > >
> > >
> > > >
> > > > I ran tests (make build ptest) at
> > > > https://github.com/mkoeppe/sage/actions/runs/65613035 .
> > > > Full logs for all builds are available at this link.
> > > >
> > > > *Debian* (jessie/buster/bullseye/sid), *Ubuntu*
> > > > (trusty/xenial/bionic/eoan/focal)m and *LinuxMint* (19.3) are mostly
> > > clean.
> > > >
> > > > Some of the doctest failures are likely known to distribution packagers
> > > > already. If fixes for these doctests are available already, now it's
> > > time
> > > > to upstream them.
> > > >
> > > > Some doctest failures, for example ubuntu-bionic-standard (
> > > > https://github.com/mkoeppe/sage/runs/542655815):
> > > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > > > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> > > >
> > > > ubuntu-eoan-standard
> > > > https://github.com/mkoeppe/sage/runs/542655826
> > > > sage -t src/sage/interfaces/giac.py  # 2 doctests failed
> > > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > > sage -t src/sage/libs/eclib/interface.py  # 1 doctest failed
> > > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > > > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> > > >
> > > > debian-buster-standard (https://github.com/mkoeppe/sage/runs/542655851)
> > > > sage -t src/sage/combinat/tutorial.py  # 2 doctests failed
> > > > sage -t src/sage/interfaces/ecm.py  # 3 doctests failed
> > > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > > sage -t src/sage/libs/libecm.pyx  # 1 doctest failed
> > > > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > > > sage -t src/sage/rings/finite_rings/element_pari_ffelt.pyx  # 1 doctest
> > > > failed
> > > > sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests
> > > failed
> > > > sage -t
> > > > src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py  # 2
> > > > doctests failed
> > > > sage -t src/sage/tests/book_stein_ent.py  # 1 doctest failed
> > > > sage -t
> > > >
> > > src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py
> > >
> > > > # 2 doctests failed
> > > > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> > > >
> > > > debian-bullseye-standard (https://github.com/mkoeppe/sage/runs/542655863
> > > )
> > > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > > sage -t src/sage/lfunctions/dokchitser.py  # 2 doctests failed
> > > > sage -t src/sage/lfunctions/pari.py  # 1 doctest failed
> > > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > > sage -t src/sage/interfaces/maxima.py  # Timed out
> > > > sage -t src

Re: [sage-release] Re: Sage 9.1.beta9 released

[Thierry]

On Mon, Mar 30, 2020 at 10:04:46PM +0800, Dima Pasechnik wrote:
> On Mon, 30 Mar 2020 at 21:47, Thierry 
> wrote:
> 
> > Hi,
> >
> > On Sun, Mar 29, 2020 at 12:50:18PM -0700, Matthias Köppe wrote:
> > > On Sunday, March 29, 2020 at 8:59:43 AM UTC-4, Volker Braun wrote:
> > > >
> > > > As always, you can get the latest beta version from the "develop" git
> > > > branch. Alternatively, the self-contained source tarball is at
> > > > http://www.sagemath.org/download-latest.html
> > > >
> > > > I don't see any major issues for 9.1 any more, so we should soon have
> > the
> > > > first rc. If you have anything that you thing should go in then now is
> > the
> > > > time to finish it up ;-)
> > > >
> > > > 6a4580546f (tag: 9.1.beta9, trac/develop) Updated SageMath version to
> > > > 9.1.beta9
> > > >
> > >
> > >
> > > Let me remark that this is the first beta that tries to use the system
> > > python3 in a venv (#27824) instead of building our own copy of python3.
> > > Tests of building from scratch or (after "make python3-clean") would be
> > > valuable.
> >
> > Do you suggest all of us to make distclean and ptestlong ?
> 
> in principle distclean should not be needed, but certainly make
> python3-clean
> and installing the corresponding “system” packages.

I am on the way to test it, however it seems that numpy, scipy etc are
not taken into account.

Ciao,
Thierry


> e.g. I don’t think we tested python (should  be python 3.7, i.e. not the
> latest) from python.org on MacOS.
> 
> Dima
> 
> 
> >
> > Ciao,
> > Thierry
> >
> >
> > >
> > > I ran tests (make build ptest) at
> > > https://github.com/mkoeppe/sage/actions/runs/65613035 .
> > > Full logs for all builds are available at this link.
> > >
> > > *Debian* (jessie/buster/bullseye/sid), *Ubuntu*
> > > (trusty/xenial/bionic/eoan/focal)m and *LinuxMint* (19.3) are mostly
> > clean.
> > >
> > > Some of the doctest failures are likely known to distribution packagers
> > > already. If fixes for these doctests are available already, now it's
> > time
> > > to upstream them.
> > >
> > > Some doctest failures, for example ubuntu-bionic-standard (
> > > https://github.com/mkoeppe/sage/runs/542655815):
> > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> > >
> > > ubuntu-eoan-standard
> > > https://github.com/mkoeppe/sage/runs/542655826
> > > sage -t src/sage/interfaces/giac.py  # 2 doctests failed
> > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > sage -t src/sage/libs/eclib/interface.py  # 1 doctest failed
> > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> > >
> > > debian-buster-standard (https://github.com/mkoeppe/sage/runs/542655851)
> > > sage -t src/sage/combinat/tutorial.py  # 2 doctests failed
> > > sage -t src/sage/interfaces/ecm.py  # 3 doctests failed
> > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > sage -t src/sage/libs/libecm.pyx  # 1 doctest failed
> > > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > > sage -t src/sage/rings/finite_rings/element_pari_ffelt.pyx  # 1 doctest
> > > failed
> > > sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests
> > failed
> > > sage -t
> > > src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py  # 2
> > > doctests failed
> > > sage -t src/sage/tests/book_stein_ent.py  # 1 doctest failed
> > > sage -t
> > >
> > src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py
> >
> > > # 2 doctests failed
> > > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> > >
> > > debian-bullseye-standard (https://github.com/mkoeppe/sage/runs/542655863
> > )
> > > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > > sage -t src/sage/lfunctions/dokchitser.py  # 2 doctests failed
> > > sage -t src/sage/lfunctions/pari.py  # 1 doctest failed
> > > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > > sage -t src/sage/interfaces/maxima.py  # Timed out
> > > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > > sage -t src/sage/rings/number_field/number_field.py  # 8 doctests failed
> > > sage -t src/sage/rings/number_field/number_field_ideal.py  # 2 doctests
> > > failed
> > > sage -t src/sage/rings/number_field/unit_group.py  # 1 doctest failed
> > > sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 do

Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

On Mon, 30 Mar 2020 at 21:47, Thierry 
wrote:

> Hi,
>
> On Sun, Mar 29, 2020 at 12:50:18PM -0700, Matthias Köppe wrote:
> > On Sunday, March 29, 2020 at 8:59:43 AM UTC-4, Volker Braun wrote:
> > >
> > > As always, you can get the latest beta version from the "develop" git
> > > branch. Alternatively, the self-contained source tarball is at
> > > http://www.sagemath.org/download-latest.html
> > >
> > > I don't see any major issues for 9.1 any more, so we should soon have
> the
> > > first rc. If you have anything that you thing should go in then now is
> the
> > > time to finish it up ;-)
> > >
> > > 6a4580546f (tag: 9.1.beta9, trac/develop) Updated SageMath version to
> > > 9.1.beta9
> > >
> >
> >
> > Let me remark that this is the first beta that tries to use the system
> > python3 in a venv (#27824) instead of building our own copy of python3.
> > Tests of building from scratch or (after "make python3-clean") would be
> > valuable.
>
> Do you suggest all of us to make distclean and ptestlong ?

in principle distclean should not be needed, but certainly make
python3-clean
and installing the corresponding “system” packages.

e.g. I don’t think we tested python (should  be python 3.7, i.e. not the
latest) from python.org on MacOS.

Dima


>
> Ciao,
> Thierry
>
>
> >
> > I ran tests (make build ptest) at
> > https://github.com/mkoeppe/sage/actions/runs/65613035 .
> > Full logs for all builds are available at this link.
> >
> > *Debian* (jessie/buster/bullseye/sid), *Ubuntu*
> > (trusty/xenial/bionic/eoan/focal)m and *LinuxMint* (19.3) are mostly
> clean.
> >
> > Some of the doctest failures are likely known to distribution packagers
> > already. If fixes for these doctests are available already, now it's
> time
> > to upstream them.
> >
> > Some doctest failures, for example ubuntu-bionic-standard (
> > https://github.com/mkoeppe/sage/runs/542655815):
> > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> >
> > ubuntu-eoan-standard
> > https://github.com/mkoeppe/sage/runs/542655826
> > sage -t src/sage/interfaces/giac.py  # 2 doctests failed
> > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > sage -t src/sage/libs/eclib/interface.py  # 1 doctest failed
> > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> >
> > debian-buster-standard (https://github.com/mkoeppe/sage/runs/542655851)
> > sage -t src/sage/combinat/tutorial.py  # 2 doctests failed
> > sage -t src/sage/interfaces/ecm.py  # 3 doctests failed
> > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > sage -t src/sage/libs/libecm.pyx  # 1 doctest failed
> > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > sage -t src/sage/rings/finite_rings/element_pari_ffelt.pyx  # 1 doctest
> > failed
> > sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests
> failed
> > sage -t
> > src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py  # 2
> > doctests failed
> > sage -t src/sage/tests/book_stein_ent.py  # 1 doctest failed
> > sage -t
> >
> src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py
>
> > # 2 doctests failed
> > sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> >
> > debian-bullseye-standard (https://github.com/mkoeppe/sage/runs/542655863
> )
> > sage -t src/sage/interfaces/r.py  # 1 doctest failed
> > sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> > sage -t src/sage/lfunctions/dokchitser.py  # 2 doctests failed
> > sage -t src/sage/lfunctions/pari.py  # 1 doctest failed
> > sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> > sage -t src/sage/interfaces/maxima.py  # Timed out
> > sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> > sage -t src/sage/rings/number_field/number_field.py  # 8 doctests failed
> > sage -t src/sage/rings/number_field/number_field_ideal.py  # 2 doctests
> > failed
> > sage -t src/sage/rings/number_field/unit_group.py  # 1 doctest failed
> > sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests
> failed
> > sage -t src/sage/rings/polynomial/polynomial_quotient_ring.py  # 2
> doctests
> > failed
> > sage -t src/sage/rings/number_field/number_field_element.pyx  # Timed out
> > sage -t src/sage/schemes/elliptic_curves/ell_number_field.py  # 3
> doctests
> > failed
> > sage -t src/sage/schemes/elliptic_curves/height.py  # 6 doctests failed
> > sage -t src/sage/schemes/plane_conics/con_n

Re: [sage-release] Re: Sage 9.1.beta9 released

[Thierry]

Hi,

On Sun, Mar 29, 2020 at 12:50:18PM -0700, Matthias Köppe wrote:
> On Sunday, March 29, 2020 at 8:59:43 AM UTC-4, Volker Braun wrote:
> >
> > As always, you can get the latest beta version from the "develop" git 
> > branch. Alternatively, the self-contained source tarball is at 
> > http://www.sagemath.org/download-latest.html 
> >
> > I don't see any major issues for 9.1 any more, so we should soon have the 
> > first rc. If you have anything that you thing should go in then now is the 
> > time to finish it up ;-)
> >
> > 6a4580546f (tag: 9.1.beta9, trac/develop) Updated SageMath version to 
> > 9.1.beta9
> >
> 
> 
> Let me remark that this is the first beta that tries to use the system 
> python3 in a venv (#27824) instead of building our own copy of python3. 
> Tests of building from scratch or (after "make python3-clean") would be 
> valuable.

Do you suggest all of us to make distclean and ptestlong ?

Ciao,
Thierry


> 
> I ran tests (make build ptest) at 
> https://github.com/mkoeppe/sage/actions/runs/65613035 . 
> Full logs for all builds are available at this link.
> 
> *Debian* (jessie/buster/bullseye/sid), *Ubuntu* 
> (trusty/xenial/bionic/eoan/focal)m and *LinuxMint* (19.3) are mostly clean.
> 
> Some of the doctest failures are likely known to distribution packagers 
> already. If fixes for these doctests are available already, now it's time 
> to upstream them.
> 
> Some doctest failures, for example ubuntu-bionic-standard (
> https://github.com/mkoeppe/sage/runs/542655815):
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> 
> ubuntu-eoan-standard
> https://github.com/mkoeppe/sage/runs/542655826
> sage -t src/sage/interfaces/giac.py  # 2 doctests failed
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/libs/eclib/interface.py  # 1 doctest failed
> sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> 
> debian-buster-standard (https://github.com/mkoeppe/sage/runs/542655851)
> sage -t src/sage/combinat/tutorial.py  # 2 doctests failed
> sage -t src/sage/interfaces/ecm.py  # 3 doctests failed
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> sage -t src/sage/libs/libecm.pyx  # 1 doctest failed
> sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> sage -t src/sage/rings/finite_rings/element_pari_ffelt.pyx  # 1 doctest 
> failed
> sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests failed
> sage -t 
> src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py  # 2 
> doctests failed
> sage -t src/sage/tests/book_stein_ent.py  # 1 doctest failed
> sage -t 
> src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py
>   
> # 2 doctests failed
> sage -t src/sage/tests/cmdline.py  # 3 doctests failed
>  
> debian-bullseye-standard (https://github.com/mkoeppe/sage/runs/542655863)
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/lfunctions/dokchitser.py  # 2 doctests failed
> sage -t src/sage/lfunctions/pari.py  # 1 doctest failed
> sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> sage -t src/sage/interfaces/maxima.py  # Timed out
> sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> sage -t src/sage/rings/number_field/number_field.py  # 8 doctests failed
> sage -t src/sage/rings/number_field/number_field_ideal.py  # 2 doctests 
> failed
> sage -t src/sage/rings/number_field/unit_group.py  # 1 doctest failed
> sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests failed
> sage -t src/sage/rings/polynomial/polynomial_quotient_ring.py  # 2 doctests 
> failed
> sage -t src/sage/rings/number_field/number_field_element.pyx  # Timed out
> sage -t src/sage/schemes/elliptic_curves/ell_number_field.py  # 3 doctests 
> failed
> sage -t src/sage/schemes/elliptic_curves/height.py  # 6 doctests failed
> sage -t src/sage/schemes/plane_conics/con_number_field.py  # 1 doctest 
> failed
> sage -t src/sage/tests/cmdline.py  # 3 doctests failed
> 
> 
> *Fedora* (26-32), *Centos* (7-8):
> 
> Fedora 26: clean
> 
> Fedora 27, 28, 29: Critical test failures in sage.combinat, likely because 
> of symmetrica https://trac.sagemath.org/ticket/29405
> 
> Fedora 30 and 31: Doctest build error related to eclib 
> 
> Fedora 32: Build errors with various packages. Fedora 32 already ships gcc 
> 10!
> 
> Centos 7 and 8: clean
> 
>

Re: [sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Monday, March 30, 2020 at 1:49:28 AM UTC-4, Dima Pasechnik wrote:
>
> On Mon, Mar 30, 2020 at 1:12 PM Matthias Köppe  > wrote: 
> > 
> > By the way, current homebrew does not seem to have Python 3.7.x. 
> really? 
> https://github.com/Homebrew/homebrew-core/blob/master/Formula/python.rb 
> still shows 3.7.7 
>
>
You are right. 

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[sage-release] Re: Sage 9.1.beta9 released

[Marc Mezzarobba]

Volker Braun wrote:
> I don't see any major issues for 9.1 any more, so we should soon have
> the first rc. If you have anything that you thing should go in then
> now is the time to finish it up ;-)

I'd really like #28517 to go in, because it fixes some serious issues 
reported by a user attempting to do "real" mathematics with Sage and has 
been waiting for close to 6 months... But that depends on someone being 
available to review it!

-- 
Marc

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[sage-release] Re: Sage 9.1.beta9 released

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.1.beta6 to 
9.1.beta9 gets 13 permanent errors :

--
sage -t --long src/sage/schemes/elliptic_curves/ell_number_field.py  # 5 
doctests failed
sage -t --long src/sage/schemes/elliptic_curves/height.py  # 6 doctests 
failed
sage -t --long src/sage/rings/number_field/number_field.py  # 8 doctests 
failed
sage -t --long src/sage/schemes/elliptic_curves/gp_simon.py  # 2 doctests 
failed
sage -t --long src/sage/rings/number_field/number_field_ideal.py  # 2 
doctests failed
sage -t --long src/sage/schemes/plane_conics/con_number_field.py  # 2 
doctests failed
sage -t --long src/sage/tests/gap_packages.py  # 1 doctest failed
sage -t --long src/sage/lfunctions/dokchitser.py  # 2 doctests failed
sage -t --long src/sage/rings/number_field/number_field_element.pyx  # 
Timed out
sage -t --long src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest 
failed
sage -t --long src/sage/rings/polynomial/polynomial_quotient_ring.py  # 2 
doctests failed
sage -t --long src/sage/lfunctions/pari.py  # 1 doctest failed
sage -t --long src/sage/rings/number_field/unit_group.py  # 1 doctest failed
sage -t --long src/sage/libs/glpk/error.pyx  # 1 doctest failed
sage -t --long src/sage/interfaces/tachyon.py  # 1 doctest failed
--

Re-running these tests individually gives the enclosed chkerrs.txt.

HTH,



Le dimanche 29 mars 2020 21:50:19 UTC+2, Matthias Köppe a écrit :
>
> On Sunday, March 29, 2020 at 8:59:43 AM UTC-4, Volker Braun wrote:
>>
>> As always, you can get the latest beta version from the "develop" git 
>> branch. Alternatively, the self-contained source tarball is at 
>> http://www.sagemath.org/download-latest.html 
>>
>> I don't see any major issues for 9.1 any more, so we should soon have the 
>> first rc. If you have anything that you thing should go in then now is the 
>> time to finish it up ;-)
>>
>> 6a4580546f (tag: 9.1.beta9, trac/develop) Updated SageMath version to 
>> 9.1.beta9
>>
>
>
> Let me remark that this is the first beta that tries to use the system 
> python3 in a venv (#27824) instead of building our own copy of python3. 
> Tests of building from scratch or (after "make python3-clean") would be 
> valuable.
>
>
> I ran tests (make build ptest) at 
> https://github.com/mkoeppe/sage/actions/runs/65613035 . 
> Full logs for all builds are available at this link.
>
> *Debian* (jessie/buster/bullseye/sid), *Ubuntu* 
> (trusty/xenial/bionic/eoan/focal)m and *LinuxMint* (19.3) are mostly 
> clean.
>
> Some of the doctest failures are likely known to distribution packagers 
> already. If fixes for these doctests are available already, now it's time 
> to upstream them.
>
> Some doctest failures, for example ubuntu-bionic-standard (
> https://github.com/mkoeppe/sage/runs/542655815):
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> sage -t src/sage/tests/cmdline.py  # 3 doctests failed
>
> ubuntu-eoan-standard
> https://github.com/mkoeppe/sage/runs/542655826
> sage -t src/sage/interfaces/giac.py  # 2 doctests failed
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/libs/eclib/interface.py  # 1 doctest failed
> sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> sage -t src/sage/tests/cmdline.py  # 3 doctests failed
>
> debian-buster-standard (https://github.com/mkoeppe/sage/runs/542655851)
> sage -t src/sage/combinat/tutorial.py  # 2 doctests failed
> sage -t src/sage/interfaces/ecm.py  # 3 doctests failed
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
> sage -t src/sage/libs/libecm.pyx  # 1 doctest failed
> sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
> sage -t src/sage/rings/finite_rings/element_pari_ffelt.pyx  # 1 doctest 
> failed
> sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests failed
> sage -t 
> src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py  # 2 
> doctests failed
> sage -t src/sage/tests/book_stein_ent.py  # 1 doctest failed
> sage -t 
> src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py
>   
> # 2 doctests failed
> sage -t src/sage/tests/cmdline.py  # 3 doctests failed
>  
> debian-bullseye-standard (https://github.com/mkoeppe/sage/runs/542655863)
> sage -t src/sage/interfaces/r.py  # 1 doctest failed
> sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
> sage -t src/sage/lfunctions/dokchitser.py  # 2 doctests

Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

On Mon, Mar 30, 2020 at 1:12 PM Matthias Köppe  wrote:
>
> By the way, current homebrew does not seem to have Python 3.7.x.
really?
https://github.com/Homebrew/homebrew-core/blob/master/Formula/python.rb
still shows 3.7.7


> I am not sure how to test with historical snapshots of the homebrew 
> distribution.
>
> On Monday, March 30, 2020 at 1:08:44 AM UTC-4, Matthias Köppe wrote:
>>
>> Please post config.log and output of "brew list --versions"
>>
>> On Monday, March 30, 2020 at 12:36:25 AM UTC-4, John H Palmieri wrote:
>>>
>>> On OS X with a homebrew installation of Python 3.7.7 I get some failures, 
>>> mostly to do with pari, including messages like this:
>>>
>>> PARI/GP ERROR:
>>>   ***   bug in PARI/GP (Segmentation Fault), please report.
>>>

>
>
>
>
>
> --
> You received this message because you are subscribed to the Google Groups 
> "sage-release" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to sage-release+unsubscr...@googlegroups.com.
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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

By the way, current homebrew does not seem to have Python 3.7.x. 
I am not sure how to test with historical snapshots of the homebrew 
distribution.

On Monday, March 30, 2020 at 1:08:44 AM UTC-4, Matthias Köppe wrote:
>
> Please post config.log and output of "brew list --versions"
>
> On Monday, March 30, 2020 at 12:36:25 AM UTC-4, John H Palmieri wrote:
>>
>> On OS X with a homebrew installation of Python 3.7.7 I get some failures, 
>> mostly to do with pari, including messages like this:
>>
>> PARI/GP ERROR:
>>   ***   bug in PARI/GP (Segmentation Fault), please report.
>>
>>
>>>


 

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[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

Please post config.log and output of "brew list --versions"

On Monday, March 30, 2020 at 12:36:25 AM UTC-4, John H Palmieri wrote:
>
> On OS X with a homebrew installation of Python 3.7.7 I get some failures, 
> mostly to do with pari, including messages like this:
>
> PARI/GP ERROR:
>   ***   bug in PARI/GP (Segmentation Fault), please report.
>
>
> and this:
>
> fatal error: 'gmp.h' file not found
> #include "gmp.h"
>  ^~~
> 1 error generated.
>
> and this:
>
> RuntimeError: command 'gcc' failed with exit status 1
> ld: library not found for -lmpfr
> clang: error: linker command failed with exit code 1 (use -v to see 
> invocation)
>
> "System" packages being used, according to config.log:
>
> boost, boost_cropped, bzip2, cmake, curl, freetype, gcc, gfortran, git, 
> gmp, iconv, isl, libffi, libgd, libpng, mpc, mpfi, mpfr, mpir, ncurses, 
> ninja_build, patch, pcre,pkgconf, python, sqlite, xz, yasm, zeromq, zlib
>
> gsl, openblas, r, and readline are also installed via homebrew, but 
> ./configure doesn't seem to like them.
>
> Failures:
>
> --
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_number_field.py  # 19 doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_rational_field.py  # 31 doctests failed
> sage -t --long --warn-long 72.2 src/sage/misc/sagedoc.py  # 2 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/doctest/sources.py  # 1 doctest 
> failed
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/height.py  # 6 doctests failed
> sage -t --long --warn-long 72.2 src/sage/symbolic/expression.pyx  # 1 
> doctest failed
> sage -t --long --warn-long 72.2 
> src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py
>   
> # 9 doctests failed
> sage -t --long --warn-long 72.2 src/sage/tests/cmdline.py  # 7 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/modular/modform/element.py  # 44 
> doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/rings/number_field/number_field.py  # 2 doctests failed
> sage -t --long --warn-long 72.2 src/sage/combinat/tableau_tuple.py  # 4 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/arith/misc.py  # 8 doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/modular/modform_hecketriangle/readme.py  # 20 doctests failed
> sage -t --long --warn-long 72.2 src/sage/interfaces/maxima_abstract.py  # 
> 3 doctests failed
> sage -t --long --warn-long 72.2 src/sage/modular/abvar/abvar.py  # 1 
> doctest failed
> sage -t --long --warn-long 72.2 src/sage/structure/element.pyx  # 44 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/modular/abvar/lseries.py  # 11 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/doctest/forker.py  # 1 doctest 
> failed
> sage -t --long --warn-long 72.2 src/sage/misc/sageinspect.py  # 35 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/calculus/calculus.py  # 4 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/quadratic_forms/genera/genus.py  
> # 4 doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/geometry/polyhedron/combinatorial_polyhedron/conversions.pyx  # 24 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/graphs/connectivity.pyx  # 2 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/misc/cachefunc.pyx  # 54 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/misc/cython.py  # 19 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/plot/line.py  # 2 doctests failed
> sage -t --long --warn-long 72.2 src/sage/modular/modform/constructor.py  # 
> 1 doctest failed
> sage -t --long --warn-long 72.2 src/sage/misc/randstate.pyx  # 24 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/modules/free_module_element.pyx  
> # 3 doctests failed
> sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/BSD.py  # 
> 3 doctests failed
> sage -t --long --warn-long 72.2 src/sage/combinat/partition_tuple.py  # 8 
> doctests failed
> sage -t --long --warn-long 72.2 
> src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/elliptic_curves.rst
>   
> # 1 doctest failed
> sage -t --long --warn-long 72.2 src/sage/repl/ipython_extension.py  # 2 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/interfaces/expect.py  # 3 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/interfaces/gp.py  # 110 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/lfunctions/zero_sums.pyx  # 3 
> doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/rings/polynomial/polynomial_ring.py  # 1 doctest failed
> sage -t --long --warn-long 72.2 src/sage/parallel/decorate.py  # 7 
> doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/lseries_ell.py  # 6 doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/gp_s

Re: [sage-release] Re: Sage 9.1.beta9 released

[Dima Pasechnik]

Could it be that gcc in Homebrew gets picked to compile C/C++ code?

On Mon, Mar 30, 2020 at 12:36 PM John H Palmieri  wrote:
>
> On OS X with a homebrew installation of Python 3.7.7 I get some failures, 
> mostly to do with pari, including messages like this:
>
> PARI/GP ERROR:
>   ***   bug in PARI/GP (Segmentation Fault), please report.
>
>
> and this:
>
> fatal error: 'gmp.h' file not found
> #include "gmp.h"
>  ^~~
> 1 error generated.
>
> and this:
>
> RuntimeError: command 'gcc' failed with exit status 1
> ld: library not found for -lmpfr
> clang: error: linker command failed with exit code 1 (use -v to see 
> invocation)
>
> "System" packages being used, according to config.log:
>
> boost, boost_cropped, bzip2, cmake, curl, freetype, gcc, gfortran, git, gmp, 
> iconv, isl, libffi, libgd, libpng, mpc, mpfi, mpfr, mpir, ncurses, 
> ninja_build, patch, pcre,pkgconf, python, sqlite, xz, yasm, zeromq, zlib
>
> gsl, openblas, r, and readline are also installed via homebrew, but 
> ./configure doesn't seem to like them.
>
> Failures:
>
> --
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_number_field.py  # 19 doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/ell_rational_field.py  # 31 doctests failed
> sage -t --long --warn-long 72.2 src/sage/misc/sagedoc.py  # 2 doctests failed
> sage -t --long --warn-long 72.2 src/sage/doctest/sources.py  # 1 doctest 
> failed
> sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/height.py  # 
> 6 doctests failed
> sage -t --long --warn-long 72.2 src/sage/symbolic/expression.pyx  # 1 doctest 
> failed
> sage -t --long --warn-long 72.2 
> src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py
>   # 9 doctests failed
> sage -t --long --warn-long 72.2 src/sage/tests/cmdline.py  # 7 doctests failed
> sage -t --long --warn-long 72.2 src/sage/modular/modform/element.py  # 44 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/rings/number_field/number_field.py  
> # 2 doctests failed
> sage -t --long --warn-long 72.2 src/sage/combinat/tableau_tuple.py  # 4 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/arith/misc.py  # 8 doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/modular/modform_hecketriangle/readme.py  # 20 doctests failed
> sage -t --long --warn-long 72.2 src/sage/interfaces/maxima_abstract.py  # 3 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/modular/abvar/abvar.py  # 1 doctest 
> failed
> sage -t --long --warn-long 72.2 src/sage/structure/element.pyx  # 44 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/modular/abvar/lseries.py  # 11 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/doctest/forker.py  # 1 doctest failed
> sage -t --long --warn-long 72.2 src/sage/misc/sageinspect.py  # 35 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/calculus/calculus.py  # 4 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/quadratic_forms/genera/genus.py  # 4 
> doctests failed
> sage -t --long --warn-long 72.2 
> src/sage/geometry/polyhedron/combinatorial_polyhedron/conversions.pyx  # 24 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/graphs/connectivity.pyx  # 2 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/misc/cachefunc.pyx  # 54 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/misc/cython.py  # 19 doctests failed
> sage -t --long --warn-long 72.2 src/sage/plot/line.py  # 2 doctests failed
> sage -t --long --warn-long 72.2 src/sage/modular/modform/constructor.py  # 1 
> doctest failed
> sage -t --long --warn-long 72.2 src/sage/misc/randstate.pyx  # 24 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/modules/free_module_element.pyx  # 3 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/BSD.py  # 3 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/combinat/partition_tuple.py  # 8 
> doctests failed
> sage -t --long --warn-long 72.2 
> src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/elliptic_curves.rst
>   # 1 doctest failed
> sage -t --long --warn-long 72.2 src/sage/repl/ipython_extension.py  # 2 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/interfaces/expect.py  # 3 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/interfaces/gp.py  # 110 doctests 
> failed
> sage -t --long --warn-long 72.2 src/sage/lfunctions/zero_sums.pyx  # 3 
> doctests failed
> sage -t --long --warn-long 72.2 src/sage/rings/polynomial/polynomial_ring.py  
> # 1 doctest failed
> sage -t --long --warn-long 72.2 src/sage/parallel/decorate.py  # 7 doctests 
> failed
> sage -t --long --warn-long 72.2 
> src/sage/schemes/elliptic_curves/lseries_ell.py  # 6 doctests failed
> sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/gp_simon.py  
> # 5 doctests fa

[sage-release] Re: Sage 9.1.beta9 released

[John H Palmieri]

On OS X with a homebrew installation of Python 3.7.7 I get some failures, 
mostly to do with pari, including messages like this:

PARI/GP ERROR:
  ***   bug in PARI/GP (Segmentation Fault), please report.


and this:

fatal error: 'gmp.h' file not found
#include "gmp.h"
 ^~~
1 error generated.

and this:

RuntimeError: command 'gcc' failed with exit status 1
ld: library not found for -lmpfr
clang: error: linker command failed with exit code 1 (use -v to see 
invocation)

"System" packages being used, according to config.log:

boost, boost_cropped, bzip2, cmake, curl, freetype, gcc, gfortran, git, 
gmp, iconv, isl, libffi, libgd, libpng, mpc, mpfi, mpfr, mpir, ncurses, 
ninja_build, patch, pcre,pkgconf, python, sqlite, xz, yasm, zeromq, zlib

gsl, openblas, r, and readline are also installed via homebrew, but 
./configure doesn't seem to like them.

Failures:

--
sage -t --long --warn-long 72.2 
src/sage/schemes/elliptic_curves/ell_number_field.py  # 19 doctests failed
sage -t --long --warn-long 72.2 
src/sage/schemes/elliptic_curves/ell_rational_field.py  # 31 doctests failed
sage -t --long --warn-long 72.2 src/sage/misc/sagedoc.py  # 2 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/doctest/sources.py  # 1 doctest 
failed
sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/height.py  
# 6 doctests failed
sage -t --long --warn-long 72.2 src/sage/symbolic/expression.pyx  # 1 
doctest failed
sage -t --long --warn-long 72.2 
src/sage/tests/books/computational-mathematics-with-sagemath/integration_doctest.py
  
# 9 doctests failed
sage -t --long --warn-long 72.2 src/sage/tests/cmdline.py  # 7 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/modular/modform/element.py  # 44 
doctests failed
sage -t --long --warn-long 72.2 
src/sage/rings/number_field/number_field.py  # 2 doctests failed
sage -t --long --warn-long 72.2 src/sage/combinat/tableau_tuple.py  # 4 
doctests failed
sage -t --long --warn-long 72.2 src/sage/arith/misc.py  # 8 doctests failed
sage -t --long --warn-long 72.2 
src/sage/modular/modform_hecketriangle/readme.py  # 20 doctests failed
sage -t --long --warn-long 72.2 src/sage/interfaces/maxima_abstract.py  # 3 
doctests failed
sage -t --long --warn-long 72.2 src/sage/modular/abvar/abvar.py  # 1 
doctest failed
sage -t --long --warn-long 72.2 src/sage/structure/element.pyx  # 44 
doctests failed
sage -t --long --warn-long 72.2 src/sage/modular/abvar/lseries.py  # 11 
doctests failed
sage -t --long --warn-long 72.2 src/sage/doctest/forker.py  # 1 doctest 
failed
sage -t --long --warn-long 72.2 src/sage/misc/sageinspect.py  # 35 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/calculus/calculus.py  # 4 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/quadratic_forms/genera/genus.py  # 
4 doctests failed
sage -t --long --warn-long 72.2 
src/sage/geometry/polyhedron/combinatorial_polyhedron/conversions.pyx  # 24 
doctests failed
sage -t --long --warn-long 72.2 src/sage/graphs/connectivity.pyx  # 2 
doctests failed
sage -t --long --warn-long 72.2 src/sage/misc/cachefunc.pyx  # 54 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/misc/cython.py  # 19 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/plot/line.py  # 2 doctests failed
sage -t --long --warn-long 72.2 src/sage/modular/modform/constructor.py  # 
1 doctest failed
sage -t --long --warn-long 72.2 src/sage/misc/randstate.pyx  # 24 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/modules/free_module_element.pyx  # 
3 doctests failed
sage -t --long --warn-long 72.2 src/sage/schemes/elliptic_curves/BSD.py  # 
3 doctests failed
sage -t --long --warn-long 72.2 src/sage/combinat/partition_tuple.py  # 8 
doctests failed
sage -t --long --warn-long 72.2 
src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/elliptic_curves.rst
  
# 1 doctest failed
sage -t --long --warn-long 72.2 src/sage/repl/ipython_extension.py  # 2 
doctests failed
sage -t --long --warn-long 72.2 src/sage/interfaces/expect.py  # 3 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/interfaces/gp.py  # 110 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/lfunctions/zero_sums.pyx  # 3 
doctests failed
sage -t --long --warn-long 72.2 
src/sage/rings/polynomial/polynomial_ring.py  # 1 doctest failed
sage -t --long --warn-long 72.2 src/sage/parallel/decorate.py  # 7 doctests 
failed
sage -t --long --warn-long 72.2 
src/sage/schemes/elliptic_curves/lseries_ell.py  # 6 doctests failed
sage -t --long --warn-long 72.2 
src/sage/schemes/elliptic_curves/gp_simon.py  # 5 doctests failed
sage -t --long --warn-long 72.2 src/sage/features/__init__.py  # 2 doctests 
failed
sage -t --long --warn-long 72.2 src/sage/matrix/matrix0.pyx  # 2 doctests 
failed
sage -t --long --warn-long 72.2 
src/sage/modular/modform_hecketriangle/element.py  # 29 doctests failed
sage -t --long --warn-long 72.2 
src/sage/groups/perm_g

[sage-release] Re: Sage 9.1.beta9 released

[Matthias Köppe]

On Sunday, March 29, 2020 at 8:59:43 AM UTC-4, Volker Braun wrote:
>
> As always, you can get the latest beta version from the "develop" git 
> branch. Alternatively, the self-contained source tarball is at 
> http://www.sagemath.org/download-latest.html 
>
> I don't see any major issues for 9.1 any more, so we should soon have the 
> first rc. If you have anything that you thing should go in then now is the 
> time to finish it up ;-)
>
> 6a4580546f (tag: 9.1.beta9, trac/develop) Updated SageMath version to 
> 9.1.beta9
>


Let me remark that this is the first beta that tries to use the system 
python3 in a venv (#27824) instead of building our own copy of python3. 
Tests of building from scratch or (after "make python3-clean") would be 
valuable.


I ran tests (make build ptest) at 
https://github.com/mkoeppe/sage/actions/runs/65613035 . 
Full logs for all builds are available at this link.

*Debian* (jessie/buster/bullseye/sid), *Ubuntu* 
(trusty/xenial/bionic/eoan/focal)m and *LinuxMint* (19.3) are mostly clean.

Some of the doctest failures are likely known to distribution packagers 
already. If fixes for these doctests are available already, now it's time 
to upstream them.

Some doctest failures, for example ubuntu-bionic-standard (
https://github.com/mkoeppe/sage/runs/542655815):
sage -t src/sage/interfaces/r.py  # 1 doctest failed
sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
sage -t src/sage/tests/cmdline.py  # 3 doctests failed

ubuntu-eoan-standard
https://github.com/mkoeppe/sage/runs/542655826
sage -t src/sage/interfaces/giac.py  # 2 doctests failed
sage -t src/sage/interfaces/r.py  # 1 doctest failed
sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
sage -t src/sage/libs/eclib/interface.py  # 1 doctest failed
sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
sage -t src/sage/tests/cmdline.py  # 3 doctests failed

debian-buster-standard (https://github.com/mkoeppe/sage/runs/542655851)
sage -t src/sage/combinat/tutorial.py  # 2 doctests failed
sage -t src/sage/interfaces/ecm.py  # 3 doctests failed
sage -t src/sage/interfaces/r.py  # 1 doctest failed
sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
sage -t src/sage/libs/libecm.pyx  # 1 doctest failed
sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
sage -t src/sage/rings/finite_rings/element_pari_ffelt.pyx  # 1 doctest 
failed
sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests failed
sage -t 
src/sage/schemes/hyperelliptic_curves/hyperelliptic_finite_field.py  # 2 
doctests failed
sage -t src/sage/tests/book_stein_ent.py  # 1 doctest failed
sage -t 
src/sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py
  
# 2 doctests failed
sage -t src/sage/tests/cmdline.py  # 3 doctests failed
 
debian-bullseye-standard (https://github.com/mkoeppe/sage/runs/542655863)
sage -t src/sage/interfaces/r.py  # 1 doctest failed
sage -t src/sage/interfaces/tachyon.py  # 1 doctest failed
sage -t src/sage/lfunctions/dokchitser.py  # 2 doctests failed
sage -t src/sage/lfunctions/pari.py  # 1 doctest failed
sage -t src/sage/libs/glpk/error.pyx  # 1 doctest failed
sage -t src/sage/interfaces/maxima.py  # Timed out
sage -t src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
sage -t src/sage/rings/number_field/number_field.py  # 8 doctests failed
sage -t src/sage/rings/number_field/number_field_ideal.py  # 2 doctests 
failed
sage -t src/sage/rings/number_field/unit_group.py  # 1 doctest failed
sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests failed
sage -t src/sage/rings/polynomial/polynomial_quotient_ring.py  # 2 doctests 
failed
sage -t src/sage/rings/number_field/number_field_element.pyx  # Timed out
sage -t src/sage/schemes/elliptic_curves/ell_number_field.py  # 3 doctests 
failed
sage -t src/sage/schemes/elliptic_curves/height.py  # 6 doctests failed
sage -t src/sage/schemes/plane_conics/con_number_field.py  # 1 doctest 
failed
sage -t src/sage/tests/cmdline.py  # 3 doctests failed


*Fedora* (26-32), *Centos* (7-8):

Fedora 26: clean

Fedora 27, 28, 29: Critical test failures in sage.combinat, likely because 
of symmetrica https://trac.sagemath.org/ticket/29405

Fedora 30 and 31: Doctest build error related to eclib 

Fedora 32: Build errors with various packages. Fedora 32 already ships gcc 
10!

Centos 7 and 8: clean


*Arch Linux*: clean

*Slackware: *Build error with freetype; 
https://trac.sagemath.org/ticket/29373 needs review

*macOS:*

homebrew-macos-minimal:
sage -t src/sage/interfaces/gap.py  # 1 doctest failed
sage -t src/sage/rings/padics/padic_lattice_element.py  # 3 doctests failed
sage -t src/sage/sets/recursively_enumerated_set.pyx  # 2 doctests failed

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