Sage 9.1.beta4 released

[Volker Braun]

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 

6dbca5f8f9 (tag: 9.1.beta4, trac/develop) Updated SageMath version to 9.1.beta4

158b93057a Trac #29168: less unused imports and better .lgtm config file

e510d03069 Trac #29166: refresh the file Iwahori-Hecke

7e7d7ec56f Trac #29145: Indeterminacy locus and image of morphisms of schemes

9119443092 Trac #29123: little doc cleanup of "prime_range"

3322731dd4 Trac #29110: Make `dim` and alias for `dimension` in combinatorial polyhedron

0b88387957 Trac #29074: Better error message for polar of non-full dimensional polyhedra

ead6f554da Trac #28788: MR38: Fix documentation of spkg-configure.m4 and make output more verbose

5aac4d5055 Trac #28243: Accelerate `is_cactus()`

0324ad84af Trac #29173: fix factorization of multivariate Laurent polynomials

c1a90dee4c Trac #29163: repair the phc interface

886980a802 Trac #29155: Full-dimensional face of Polyhedron should have equations

3f9375ca99 Trac #29148: Add DESTDIR and Cygwin support for mcqd

74c913427f Trac #29144: remove deprecated stuff from tickets 22***

938564c6a4 Trac #29138: cleanup and some fixes for Free Zinbiel algebras

128c030f69 Trac #29135: extend the STL representation to unions and transforms

e8fccdff04 Trac #29134: node_number_at_depth broken for binary trees

6344f4f6de Trac #29125: `is_inscribed` depends on order of vertices

3e754d7157 Trac #29115: Fix deprecation warnings with scipy 1.4

8b9e6bbe8a Trac #29112: Implement incidence matrix for combinatorial polyhedron

61967966ff Trac #29109: update NTL to the latest version (11.4.3)

af348cfc28 Trac #29103: get rid of part of itervalues

554fa02a4c Trac #29083: first parameter of a normal method must be self

67a399edf1 Trac #29081: allow proper detection of gf2x 1.3

d5fdda348a Trac #29080: Degenerate Metric Submanifold: New features

3c75a3a245 Trac #29062: build/pkgs/python3/spkg-install: Install valgrind-python.supp in $SAGE_LOCAL, not in $SAGE_SRC

55b2e87f09 Trac #29034: let the example of set with grading (NN) know that it is infinite

0ff6921902 Trac #28880: Prepare setting up polyhedron from both Vrep and Hrep for different backends

84403fb80d Trac #28867: 1 imagemagick failing doctest in misc/latex.py

1143c8abd3 Trac #28862: Localization of integral domains

52644d49e9 Trac #28724: Polyhedron._acted_upon_ should handle left multiplication by matrices, linear transformations

8870d6bb19 Trac #25049: Add DESTDIR support for r, and other cleanup

ed7bc14f75 Trac #21811: libecl does not install with libffi 3.3 (e.g. on OpenSuSE gcc5-7, Debian 11, etc)

f4f06c6c47 Trac #29121: One-line fix for blocker ".pc files generated in src/ are not cleaned by `make misc-clean` / `make distclean`

84e623c1b2 Trac #29120: Two-line fix for "./configure is too sensitive to stray files/subdirectories"

1d465c7e3c (tag: 9.1.beta3) Updated SageMath version to 9.1.beta3

[Eric Gourgoulhon]

On Ubuntu 18.04 running on a bi-Xeon E5-2623 (8 cores) + 16 GB RAM computer:

  - incremental build (with -j16) from 9.1.beta3: OK

  - make ptestlong reports the same failure as with 9.1.beta3:

sage -t --long --warn-long 53.7 src/sage/groups/cubic_braid.py  # 1 doctest failed

Details in the attached log of the 9.1.beta3 message:

https://groups.google.com/d/msg/sage-release/xxEfql2Isgg/LzglNX04FQAJ

As with 9.1.beta3, the test is passed when run standalone.

Eric.

[David Coudert]

incremental build from 9.1.beta3 failed on mccd  on a linux fedora 28 computer.

Don’t know what to do (and hope to avoid distclean).

Let me know if more informations is needed.

Best,

David.

….

[rpy2-2.8.2.p1] user    0m6.064s

[rpy2-2.8.2.p1] sys     0m1.100s

[rpy2-2.8.2.p1] Copying package files from temporary location /home/dcoudert/sage/local/var/tmp/sage/build/rpy2-2.8.2.p1/inst to /home/dcoudert/sage/local

[rpy2-2.8.2.p1] Successfully installed rpy2-2.8.2.p1

[rpy2-2.8.2.p1] Deleting temporary build directory

[rpy2-2.8.2.p1] /home/dcoudert/sage/local/var/tmp/sage/build/rpy2-2.8.2.p1

[rpy2-2.8.2.p1] Finished installing rpy2-2.8.2.p1.spkg

cp /home/dcoudert/sage/src/bin/sage-env-config /home/dcoudert/sage/local/bin/sage-env-config

cp /home/dcoudert/sage/src/bin/sage-valgrind /home/dcoudert/sage/local/bin/sage-valgrind

cp /home/dcoudert/sage/src/bin/sage-version.sh /home/dcoudert/sage/local/bin/sage-version.sh

sage-logger -p 'sage-spkg  mcqd-1.0.p0' '/home/dcoudert/sage/logs/pkgs/mcqd-1.0.p0.log'

[mcqd-1.0.p0] Found local metadata for mcqd-1.0.p0

[mcqd-1.0.p0] Using cached file /home/dcoudert/sage/upstream/mcqd-1.0.tar.bz2

[mcqd-1.0.p0] mcqd-1.0.p0

[mcqd-1.0.p0] ====================================================

[mcqd-1.0.p0] Setting up build directory for mcqd-1.0.p0

[mcqd-1.0.p0] Finished extraction

[mcqd-1.0.p0] No patch files found in ../patches

[mcqd-1.0.p0] ****************************************************

[mcqd-1.0.p0] Host system:

[mcqd-1.0.p0] Linux musclotte 4.17.6-200.fc28.x86_64 #1 SMP Wed Jul 11 20:29:01 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

[mcqd-1.0.p0] ****************************************************

[mcqd-1.0.p0] C compiler: gcc

[mcqd-1.0.p0] C compiler version:

[mcqd-1.0.p0] Using built-in specs.

[mcqd-1.0.p0] COLLECT_GCC=/usr/bin/gcc

[mcqd-1.0.p0] COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper

[mcqd-1.0.p0] OFFLOAD_TARGET_NAMES=nvptx-none

[mcqd-1.0.p0] OFFLOAD_TARGET_DEFAULT=1

[mcqd-1.0.p0] Target: x86_64-redhat-linux

[mcqd-1.0.p0] Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,objc,obj-c++,ada,go,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --enable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

[mcqd-1.0.p0] Thread model: posix

[mcqd-1.0.p0] gcc version 8.1.1 20180712 (Red Hat 8.1.1-5) (GCC)

[mcqd-1.0.p0] ****************************************************

[mcqd-1.0.p0] Warning: No files to uninstall for 'mcqd'

[mcqd-1.0.p0] Uninstalling existing 'mcqd'

[mcqd-1.0.p0] Removing stamp file '/home/dcoudert/sage/local/var/lib/sage/installed/mcqd-1.0'

[mcqd-1.0.p0] /usr/bin/ld: mcqd.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC

[mcqd-1.0.p0] /usr/bin/ld: final link failed: Nonrepresentable section on output

[mcqd-1.0.p0] collect2: error: ld returned 1 exit status

[mcqd-1.0.p0] **********************************************************************************************************************************************************************

[mcqd-1.0.p0] Error: source file/directory libmcqd.so does not exist

[mcqd-1.0.p0] **********************************************************************************************************************************************************************

[mcqd-1.0.p0]

[mcqd-1.0.p0] real      0m1.196s

[mcqd-1.0.p0] user      0m0.919s

[mcqd-1.0.p0] sys       0m0.119s

[mcqd-1.0.p0] ************************************************************************

[mcqd-1.0.p0] Error installing package mcqd-1.0.p0

[mcqd-1.0.p0] ************************************************************************

[mcqd-1.0.p0] Please email sage-devel (http://groups.google.com/group/sage-devel)

[mcqd-1.0.p0] explaining the problem and including the log file

[mcqd-1.0.p0]   /home/dcoudert/sage/logs/pkgs/mcqd-1.0.p0.log

[mcqd-1.0.p0] Describe your computer, operating system, etc.

[mcqd-1.0.p0] If you want to try to fix the problem yourself, *don't* just cd to

[mcqd-1.0.p0] /home/dcoudert/sage/local/var/tmp/sage/build/mcqd-1.0.p0 and type 'make' or whatever is appropriate.

[mcqd-1.0.p0] Instead, the following commands setup all environment variables

[mcqd-1.0.p0] correctly and load a subshell for you to debug the error:

[mcqd-1.0.p0]   (cd '/home/dcoudert/sage/local/var/tmp/sage/build/mcqd-1.0.p0' && '/home/dcoudert/sage/sage' --sh)

[mcqd-1.0.p0] When you are done debugging, you can type "exit" to leave the subshell.

[mcqd-1.0.p0] ************************************************************************

make[3]: *** [Makefile:2202: /home/dcoudert/sage/local/var/lib/sage/installed/mcqd-1.0.p0] Error 1

make[3]: Leaving directory '/home/dcoudert/sage/build/make'

make[2]: *** [Makefile:1877: all-build] Error 2

make[2]: Leaving directory '/home/dcoudert/sage/build/make'

real    120m30.079s

user    96m9.752s

sys     8m51.791s

***************************************************************

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make all-build'):

* package:         mcqd-1.0.p0

  last build time: Feb 14 10:59

  log file:        /home/dcoudert/sage/logs/pkgs/mcqd-1.0.p0.log

  build directory: /home/dcoudert/sage/local/var/tmp/sage/build/mcqd-1.0.p0

It is safe to delete any log files and build directories, but they

contain information that is helpful for debugging build problems.

WARNING: If you now run 'make' again, the build directory of the

same version of the package will, by default, be deleted. Set the

environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: *** [Makefile:33: all-build] Error 1

make[1]: Leaving directory '/home/dcoudert/sage'

make: *** [Makefile:16: build] Error 2

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[Dima Pasechnik]

how about

./sage -f mcqd

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/FD07A497-2F71-42CB-B330-D040F17CF4C5%40gmail.com.

[David Coudert]

I tried ./sage -f mcqd    but it’s not enough :(

[sagelib-9.1.beta4] fi

[sagelib-9.1.beta4] make[2]: Leaving directory '/home/dcoudert/sage/src'

[sagelib-9.1.beta4] 

[sagelib-9.1.beta4] real        0m5.095s

[sagelib-9.1.beta4] user        0m4.396s

[sagelib-9.1.beta4] sys 0m0.584s

cp /home/dcoudert/sage/src/bin/sage-env-config /home/dcoudert/sage/local/bin/sage-env-config

sage-logger -p 'sage-spkg   mcqd-1.0.p0' '/home/dcoudert/sage/logs/pkgs/mcqd-1.0.p0.log'

[mcqd-1.0.p0] Found local metadata for mcqd-1.0.p0

[mcqd-1.0.p0] Using cached file /home/dcoudert/sage/upstream/mcqd-1.0.tar.bz2

[mcqd-1.0.p0] mcqd-1.0.p0

[mcqd-1.0.p0] ====================================================

[mcqd-1.0.p0] Setting up build directory for mcqd-1.0.p0

[mcqd-1.0.p0] Finished extraction

[mcqd-1.0.p0] No patch files found in ../patches

[mcqd-1.0.p0] ****************************************************

[mcqd-1.0.p0] Host system:

[mcqd-1.0.p0] Linux musclotte 4.17.6-200.fc28.x86_64 #1 SMP Wed Jul 11 20:29:01 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

[mcqd-1.0.p0] ****************************************************

[mcqd-1.0.p0] C compiler: gcc

[mcqd-1.0.p0] C compiler version:

[mcqd-1.0.p0] Using built-in specs.

[mcqd-1.0.p0] COLLECT_GCC=/usr/bin/gcc

[mcqd-1.0.p0] COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper

[mcqd-1.0.p0] OFFLOAD_TARGET_NAMES=nvptx-none

[mcqd-1.0.p0] OFFLOAD_TARGET_DEFAULT=1

[mcqd-1.0.p0] Target: x86_64-redhat-linux

[mcqd-1.0.p0] Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,objc,obj-c++,ada,go,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --enable-libmpx --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux

[mcqd-1.0.p0] Thread model: posix

[mcqd-1.0.p0] gcc version 8.1.1 20180712 (Red Hat 8.1.1-5) (GCC) 

[mcqd-1.0.p0] ****************************************************

[mcqd-1.0.p0] Package 'mcqd' is currently not installed

[mcqd-1.0.p0] No legacy uninstaller found for 'mcqd'; nothing to do

[mcqd-1.0.p0] /usr/bin/ld: mcqd.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC

[mcqd-1.0.p0] /usr/bin/ld: final link failed: Nonrepresentable section on output

[mcqd-1.0.p0] collect2: error: ld returned 1 exit status

[mcqd-1.0.p0] ***********************************************************************************************************************************************************************************

[mcqd-1.0.p0] Error: source file/directory libmcqd.so does not exist

[mcqd-1.0.p0] ***********************************************************************************************************************************************************************************

[mcqd-1.0.p0] 

[mcqd-1.0.p0] real      0m0.386s

[mcqd-1.0.p0] user      0m0.139s

[mcqd-1.0.p0] sys       0m0.056s

[mcqd-1.0.p0] ************************************************************************

[mcqd-1.0.p0] Error installing package mcqd-1.0.p0

[mcqd-1.0.p0] ************************************************************************

[mcqd-1.0.p0] Please email sage-devel (http://groups.google.com/group/sage-devel)

[mcqd-1.0.p0] explaining the problem and including the log file

[mcqd-1.0.p0]   /home/dcoudert/sage/logs/pkgs/mcqd-1.0.p0.log

[mcqd-1.0.p0] Describe your computer, operating system, etc.

[mcqd-1.0.p0] If you want to try to fix the problem yourself, *don't* just cd to

[mcqd-1.0.p0] /home/dcoudert/sage/local/var/tmp/sage/build/mcqd-1.0.p0 and type 'make' or whatever is appropriate.

[mcqd-1.0.p0] Instead, the following commands setup all environment variables

[mcqd-1.0.p0] correctly and load a subshell for you to debug the error:

[mcqd-1.0.p0]   (cd '/home/dcoudert/sage/local/var/tmp/sage/build/mcqd-1.0.p0' && '/home/dcoudert/sage/sage' --sh)

[mcqd-1.0.p0] When you are done debugging, you can type "exit" to leave the subshell.

[mcqd-1.0.p0] ************************************************************************

make[1]: *** [Makefile:2201: /home/dcoudert/sage/local/var/lib/sage/installed/mcqd-1.0.p0] Error 1

make[1]: Leaving directory '/home/dcoudert/sage/build/make'

real    0m6.293s

user    0m5.092s

sys     0m0.877s

***************************************************************

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make mcqd'):

* package:         mcqd-1.0.p0

  last build time: Feb 14 15:06

  log file:        /home/dcoudert/sage/logs/pkgs/mcqd-1.0.p0.log

  build directory: /home/dcoudert/sage/local/var/tmp/sage/build/mcqd-1.0.p0

It is safe to delete any log files and build directories, but they

contain information that is helpful for debugging build problems.

WARNING: If you now run 'make' again, the build directory of the

same version of the package will, by default, be deleted. Set the

environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make: *** [Makefile:33: mcqd] Error 1

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq2xfjwtbpa1MP%3DL1hgd%3D18GVixKCd%2BiA6WTzEdMqKhwOw%40mail.gmail.com.

[Dima Pasechnik]

mcqd needs an update of its spkg-install etc, see
https://trac.sagemath.org/ticket/29197

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/0BA93A2A-C460-42C6-939D-458D4CBC5EDB%40gmail.com.

[Thierry Dumont]

On Ubuntu 19-10:
- incremental build (with -j4) from 9.1.beta3: OK

- make ptestlong :

----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM:

• I was unable to upgrade 9.1.beta3 + #21811 to this version, the
  build failing to find the libraries for M4RI (that were present).
  This persisted after reinstallation of these libraries, and even
  after ./configure. I succeeeded by rebuilding from scratch (i. e.
  after make distclean).
• make testallong (i. e. serially) gives me a new permanent error :

Running doctests with ID 2020-02-15-15-03-08-7add6b7f.
Git branch: develop
Using --optional=build,dochtml,dot2tex,external,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,sage
External software to be detected: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,scilab

External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,mathematica,pandoc

File	Result	P/T
src/sage/numerical/backends/glpk_backend.pyx	1 doctest failed	P
src/sage/libs/glpk/error.pyx	1 doctest failed	P
src/sage/databases/findstat.py	8 doctests failed	T
src/sage/plot/animate.py	7 doctests failed	T
src/sage/combinat/tutorial.py	1 doctest failed	T
src/sage/tests/gap_packages.py	1 doctest failed	P
src/sage/matrix/matrix_double_dense.pyx	1 doctest failed	P

Details for matrix_double_dense:

sage -t --long --warn-long 50.1 src/sage/matrix/matrix_double_dense.pyx
**********************************************************************
File "src/sage/matrix/matrix_double_dense.pyx", line 2523, in sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary
Failed example:
    P.is_unitary(algorithm='orthonormal')
Expected:
    Traceback (most recent call last):
    ...
    error: ((lwork==-1)||(lwork >= MAX(1,2*n))) failed for 3rd keyword lwork: zgees:lwork=0
Got:
    <BLANKLINE>
    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary[23]>", line 1, in <module>
        P.is_unitary(algorithm='orthonormal')
      File "sage/matrix/matrix_double_dense.pyx", line 2574, in sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary (build/cythonized/sage/matrix/matrix_double_dense.c:16169)
        _, T = self.schur(base_ring=sage.rings.complex_double.CDF)
      File "sage/matrix/matrix_double_dense.pyx", line 3274, in sage.matrix.matrix_double_dense.Matrix_double_dense.schur (build/cythonized/sage/matrix/matrix_double_dense.c:19291)
        T._matrix_numpy, Q._matrix_numpy = scipy.linalg.schur(self._matrix_numpy, output=format)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/scipy/linalg/decomp_schur.py", line 139, in schur
        result = gees(lambda x: None, a1, lwork=-1)
    ValueError: On entry to ZGEES parameter number 6 had an illegal value
**********************************************************************
1 item had failures:
   1 of  29 in sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary
    [650 tests, 1 failure, 1.01 s]
----------------------------------------------------------------------
sage -t --long --warn-long 50.1 src/sage/matrix/matrix_double_dense.pyx  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 1.1 seconds
    cpu time: 1.0 seconds
    cumulative wall time: 1.0 seconds

The other permanent errors have already been reported multiple times.

HTH,

[Emmanuel Charpentier]

On a slightly smaller machine (Debin testing on core i5 + 8 GB RAM), 9.1.beta4 can be rebuilt after make distclean; a serial make testalllong gives 8 transient and one permanent failures:

Using --optional=build,dochtml,dot2tex,external,fricas,giacpy_sage,libsemigroups,memlimit,sage

External software to be detected: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,scilab

External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,mathematica,octave,pandoc

File	Result	P/T

src/sage/matrix/matrix_double_dense.pyx

1 doctest failed

P

src/sage/databases/findstat.py

8 doctests failed

T

src/sage/combinat/tutorial.py	1 doctest failed	T
src/sage/plot/animate.py	7 doctests failed	T

src/sage/interfaces/octave.py	3 doctests failed	T
src/sage/interfaces/magma_free.py	2 doctests failed	T
src/doc/en/constructions/interface_issues.rst	1 doctest failed	T
src/doc/en/constructions/linear_algebra.rst	1 doctest failed	T
src/doc/en/developer/coding_in_other.rst	1 doctest failed	T

The failure on matrix_double_dense is new on this machine:

sage -t --long src/sage/matrix/matrix_double_dense.pyx
**********************************************************************
File "src/sage/matrix/matrix_double_dense.pyx", line 2523, in sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary
Failed example:
    P.is_unitary(algorithm='orthonormal')
Expected:
    Traceback (most recent call last):
    ...
    error: ((lwork==-1)||(lwork >= MAX(1,2*n))) failed for 3rd keyword lwork: zgees:lwork=0
Got:
    <BLANKLINE>
    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary[23]>", line 1, in <module>
        P.is_unitary(algorithm='orthonormal')
      File "sage/matrix/matrix_double_dense.pyx", line 2574, in sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary (build/cythonized/sage/matrix/matrix_double_dense.c:16169)
        _, T = self.schur(base_ring=sage.rings.complex_double.CDF)
      File "sage/matrix/matrix_double_dense.pyx", line 3274, in sage.matrix.matrix_double_dense.Matrix_double_dense.schur (build/cythonized/sage/matrix/matrix_double_dense.c:19291)
        T._matrix_numpy, Q._matrix_numpy = scipy.linalg.schur(self._matrix_numpy, output=format)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/scipy/linalg/decomp_schur.py", line 139, in schur
        result = gees(lambda x: None, a1, lwork=-1)
    ValueError: On entry to ZGEES parameter number 6 had an illegal value
**********************************************************************
1 item had failures:
   1 of  29 in sage.matrix.matrix_double_dense.Matrix_double_dense.is_unitary
    [650 tests, 1 failure, 1.20 s]

HTH,

[Emmanuel Charpentier]

On the same setup, a parallel ptestalllong passes, leaving one permanent and nine
transient failures:

Using --optional=build,dochtml,dot2tex,external,fricas,giacpy_sage,libsemigroups,memlimit,sage

External software to be detected: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,scilab

External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,mathematica,octave,pandoc

File	Result	P/T

src/sage/interfaces/magma_free.py

2 doctests failed

T

src/sage/plot/animate.py	7 doctests failed	T
src/sage/databases/findstat.py	8 doctests failed	T
src/sage/combinat/tutorial.py	1 doctest failed	T

src/doc/en/constructions/linear_algebra.rst

1 doctest failed

T

src/sage/interfaces/octave.py

3 doctests failed

T

src/doc/en/constructions/interface_issues.rst

1 doctest failed

T

src/sage/matrix/matrix_double_dense.pyx

1 doctest failed

P

src/doc/en/developer/coding_in_other.rst

1 doctest failed

T

The permanent error on matrix_double_dense.pyx is the same as
aalready reported.

HTH,

[Sébastien Labbé]

Testing various 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,sagenb

----------------------------------------------------------------------

sage -t --long src/sage/geometry/polyhedron/base.py  # Killed due to abort
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
sage -t --long src/sage/databases/findstat.py  # 8 doctests failed
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
sage -t --long src/sage/combinat/tutorial.py  # 1 doctest failed
sage -t --long src/sage/interfaces/psage.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc


Rerunning faled tests, I get:

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


The tutorial.py failure is copied below:

sage -t --long src/sage/combinat/tutorial.py
**********************************************************************
File "src/sage/combinat/tutorial.py", line 1732, in sage.combinat.tutorial
Failed example:
    oeis(L)                                       # optional -- internet
Expected:
    0: A000045: Fibonacci numbers: F(n) = F(n-1) + F(n-2) with F(0) = 0 and F(1) = 1.
    1: A212804: Expansion of (1-x)/(1-x-x^2).
    2: A132636: a(n) = Fibonacci(n) mod n^3.
Got:
    0: A000045: Fibonacci numbers: F(n) = F(n-1) + F(n-2) with F(0) = 0 and F(1) = 1.
    1: A212804: Expansion of (1-x)/(1-x-x^2).
    2: A324969: Number of unlabeled rooted identity trees with n vertices whose non-leaf terminal subtrees are all different.

**********************************************************************
1 item had failures:

   1 of 248 in sage.combinat.tutorial
    5 tests for not implemented functionality not run
    6 not tested tests not run
    1 py2 test not run
    0 tests not run because we ran out of time
    [247 tests, 1 failure, 23.87 s]

Others are tracked here: https://trac.sagemath.org/ticket/25536

[Justin C. Walker]

> On Feb 13, 2020, at 15:07 , Volker Braun <vbrau...@gmail.com> 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 ran into gfortran problems on each of my three macOS systems: 10.13.6 (2017 iMac Pro, 18 core Xeon W), 10.14.6 (2017 MPB, Quad-core Core i7), and 10.15.3 (2019 MBP, 9-core Core i9). In each case, I built from a fresh clone of the develop tree.

In each case, the build complained that there was no gfortran available, and stopped. I followed the Sage advice and ran
./sage -i gfortran
and after that, gfortran was successfully built, and via some magic, the build completed. I then built the docs and tests (‘ptestlong’) with no problems, and all tests passed on each of the three systems.

Justin

--
Justin C. Walker, Curmudgeon at Large
Director
Institute for the Enhancement of the Director's Income
--
In mathematics you don't understand
things. You just get used to them.
--John von Neumann
--