Sage 9.1.beta0 released

Volker Braun

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Jan 10, 2020, 11:19:30 AM1/10/20

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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

b8f53f72e8 (HEAD -> develop, tag: 9.1.beta0, trac/develop) Updated SageMath version to 9.1.beta0

7140d0e7bb Trac #28389: Support constructing Singular ring with ring order with 'c' or 'C'

1f04f40d45 Trac #27513: Allow custom order for edges as well as vertices for incidence matrix

5c3676468a Trac #28950: more precise assert statements

56ef6f028c Trac #28948: some preparation for ipython7

d6b83409eb Trac #28947: multiplicative Abelian groups are not GAP friendly

5762334c54 Trac #28938: remove deprecated methods in some combinatorial Hopf algebras

ae18b5d03e Trac #28937: change some doc about python3

ba2f949961 Trac #28935: infinite recursion in exponential of sparse matrices

b731e8b1af Trac #28933: no longer use _cmp_ in vectors

51e7813414 Trac #28929: HyperbolicGeodesic.plot() returns None if self is a line and boundary=False

2b596aad84 Trac #28927: DESTDIR support for libbraiding and libhomfly

6bfc8ed6d0 Trac #28909: Allow overriding "when building, check that user isn't root" for use in Docker containers with configure --enable-build-as-root

f5c516cb00 Trac #28884: spkg-configure for R

c4ed371cdf Trac #28879: spkg-configure for GSL

3047e9e8c3 Trac #28855: PolynomialRing random_element()s aren't always ring elements

da593dc5f5 Trac #28688: fix buckygen for modern C/C++

896120d9fd Trac #27870: spkg-configure.m4 for $(BLAS) (i.e. atlas and openblas)

304fe834c5 Trac #25903: fix Macaulay2 output when reading input from a file

1e5c93fadf Trac #7165: sage fails to plot a quarter circle when it should

e9db0c6dde Trac #28903: Sympy-conversion of complex numbers

2111e0063b Trac #28899: some details in rings/polynomial/

f8c7d3650d Trac #28848: Add methods for the lattice of subsets

2ec94231bf Trac #28557: julia_plot sometimes does not draw the entire julia set

c80928120c Trac #23946: Exhaust over Weil polynomials

c767179b74 Trac #28930: pyflakes fix in dynamics

1a8f1fa3fa Trac #28926: MR39: Update Developer's guide regarding pull requests

16052a5aa6 Trac #28919: spkg-configure for tachyon

1890aefa44 Trac #28914: default_mip_solver: Allow solver = a callable

ebb0d39a81 Trac #28911: Update sympy to 1.5

889d29cb9b Trac #28897: BipartiteGraph blindly trusts generic graphs

082db1579a Trac #28889: HyperbolicGeodesic.angle() returns mathematically incorrect results

3914a955ab Trac #28883: update pkgconfig to version 1.5.1

e8987e793c Trac #28646: Use CombinatorialPolyhedron to obtain faces of polyhedra

4fc6fba1e8 Trac #28311: Random failure in combinatorial_polyhedron/base.pyx

5fa32aa9f8 Trac #28175: Move optional sage optimization backends (COIN, CPLEX, Gurobi) to separate Cython packages to remove OptionalExtension problems

7afa68e7ff Trac #27953: Integral curves over finite fields: base classes

906cf147fe Trac #27424: enumeration of minimal dominating sets

3c293de084 Trac #26355: Degenerate Metric and Degenerate Metric Manifold

31cb54b779 (tag: 9.0, trac/master, master) Updated SageMath version to 9.0

Jaap Spies

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Jan 10, 2020, 4:47:17 PM1/10/20

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On Fedora 31 Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz

real 65m0,958s

user 406m25,271s
sys 21m20,069s
Sage build/upgrade complete!
make[1]: Leaving directory '/home/jaap/sagemath/sage-9.1.beta0'

----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 2418.2 seconds
cpu time: 14436.1 seconds
cumulative wall time: 18063.5 seconds
[jaap@vrede sage-9.1.beta0]$

Matthias Köppe

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Jan 10, 2020, 10:17:14 PM1/10/20

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On Friday, January 10, 2020 at 11:19:30 AM UTC-5, 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

b8f53f72e8 (HEAD -> develop, tag: 9.1.beta0, trac/develop) Updated SageMath version to 9.1.beta0 ....

5fa32aa9f8 Trac #28175: Move optional sage optimization backends (COIN, CPLEX, Gurobi) to separate Cython packages to remove OptionalExtension problems

Volker, the new packages from #28175 are missing on the mirrors.

Jaap Spies

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Jan 11, 2020, 4:48:00 AM1/11/20

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On a Raspberry Pi 4B with 4 GB memory, running on a Western Digital 500 GB SDD

real 366m47.488s

user 942m5.388s

sys 72m37.278s

Sage build/upgrade complete!

make[1]: Leaving directory '/home/pi/Downloads/sage-9.1.beta0'

pi@rasp4g:~/Downloads/sage-9.1.beta0 $

Still running make ptestlong.

Volker Braun

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Jan 11, 2020, 7:03:21 AM1/11/20

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Thanks, fixed!

Jaap Spies

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Jan 11, 2020, 7:59:09 AM1/11/20

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On Rasbian (see below)

make ptestlong ended with:

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

Total time for all tests: 28699.4 seconds

cpu time: 41119.9 seconds

cumulative wall time: 51721.1 seconds

make: *** [Makefile:178: ptestlong] Error 21

Some or most will be transient failures? I'll check.

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

sage -t --long src/sage/modular/arithgroup/congroup_gammaH.py # Killed due to segmentation fault

sage -t --long src/sage/modular/btquotients/pautomorphicform.py # Timed out

sage -t --long src/sage/rings/finite_rings/residue_field.pyx # Timed out

sage -t --long src/sage/schemes/elliptic_curves/constructor.py # Timed out

sage -t --long src/sage/schemes/elliptic_curves/gal_reps.py # Timed out

sage -t --long src/sage/rings/function_field/function_field.py # Timed out

sage -t --long src/sage/structure/coerce_dict.pyx # 1 doctest failed

sage -t --long src/sage/manifolds/differentiable/mixed_form.py # Killed due to segmentation fault

sage -t --long src/sage/schemes/hyperelliptic_curves/hyperelliptic_padic_field.py # Timed out

sage -t --long src/sage/combinat/tableau.py # Killed due to segmentation fault

sage -t --long src/sage/combinat/designs/database.py # Timed out

sage -t --long src/sage/graphs/strongly_regular_db.pyx # Killed due to segmentation fault

sage -t --long src/sage/modular/hypergeometric_motive.py # Timed out

sage -t --long src/sage/schemes/cyclic_covers/cycliccover_finite_field.py # Timed out

sage -t --long src/sage/categories/pushout.py # Timed out

sage -t --long src/sage/modular/btquotients/btquotient.py # Timed out

sage -t --long src/sage/rings/function_field/differential.py # Killed due to segmentation fault

sage -t --long src/sage/rings/valuation/valuation.py # Timed out

sage -t --long src/sage/schemes/toric/sheaf/klyachko.py # Timed out

sage -t --long src/sage/modular/pollack_stevens/padic_lseries.py # Timed out

sage -t --long src/sage/combinat/ncsym/ncsym.py # Killed due to segmentation fault

sage -t --long src/sage/misc/c3_controlled.pyx # Killed due to segmentation fault

sage -t --long src/sage/modular/local_comp/smoothchar.py # Timed out

sage -t --long src/sage/combinat/designs/block_design.py # Timed out

sage -t --long src/sage/rings/function_field/function_field_valuation.py # Timed out

sage -t --long src/sage/schemes/elliptic_curves/descent_two_isogeny.pyx # Timed out

sage -t --long src/sage/schemes/elliptic_curves/ell_torsion.py # Timed out

sage -t --long src/sage/combinat/sf/orthotriang.py # Killed due to segmentation fault

sage -t --long src/sage/modular/modform/tests.py # Killed due to segmentation fault

sage -t --long src/sage/schemes/curves/constructor.py # Killed due to segmentation fault

sage -t --long src/sage/combinat/sf/powersum.py # Killed due to segmentation fault

sage -t --long src/sage/matrix/matrix_cyclo_dense.pyx # Timed out

sage -t --long src/sage/schemes/affine/affine_morphism.py # Timed out

sage -t --long src/sage/quivers/homspace.py # Killed due to segmentation fault

sage -t --long src/sage/rings/finite_rings/finite_field_prime_modn.py # Killed due to segmentation fault

sage -t --long src/sage/rings/morphism.pyx # Timed out

sage -t --long src/sage/rings/padics/relative_extension_leaves.py # Timed out

sage -t --long src/sage/misc/weak_dict.pyx # 11 doctests failed

sage -t --long src/sage/coding/reed_muller_code.py # Timed out

sage -t --long src/doc/en/constructions/elliptic_curves.rst # Timed out

sage -t --long src/doc/en/constructions/number_fields.rst # Timed out

sage -t --long src/sage/cpython/dict_del_by_value.pyx # 1 doctest failed

sage -t --long src/sage/monoids/free_abelian_monoid.py # Killed due to segmentation fault

sage -t --long src/sage/modular/overconvergent/weightspace.py # Timed out

sage -t --long src/sage/categories/complete_discrete_valuation.py # Timed out

sage -t --long src/sage/structure/parent.pyx # Timed out

sage -t --long src/sage/rings/ring.pyx # Timed out

sage -t --long src/sage/modular/pollack_stevens/dist.pyx # Timed out

sage -t --long src/sage/rings/padics/padic_generic_element.pyx # Timed out

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

Emmanuel Charpentier

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Jan 11, 2020, 8:07:34 AM1/11/20

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On Debian testing running on core i7 + 16 GB RAM, upgrading a Python 3-based Sage 9.0 to 9.1.beta0 and running ptestalllong gets 3 permanent and 5 transient failures:

File	Result	P/T
src/sage/databases/oeis.py	1 doctest failed	T
src/sage/plot/animate.py	7 doctests failed	T
src/sage/numerical/backends/glpk_backend.pyx	1 doctest failed	P
src/sage/tests/gap_packages.py	1 doctest failed	P
src/sage/misc/latex.py	1 doctest failed	T
src/sage/libs/glpk/error.pyx	1 doctest failed	P
src/sage/repl/load.py	1 doctest failed	T
src/sage/databases/findstat.py	8 doctests failed	T

All of these failures have been reported multiple times. No new failure here.

HTH,

Emmanuel Charpentier

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Jan 11, 2020, 8:09:24 AM1/11/20

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What happens when you re-run these failed test standalone (i. e. one at a time) ?

Justin C. Walker

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Jan 11, 2020, 4:33:42 PM1/11/20

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> On Jan 10, 2020, at 08:19 , 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

Built w/o problems from fresh clones of the develop branch, on two macOS systems: 10.13.6 (2017 iMac Pro, 18-core Xeon W) and 10.14.6 (2017 MBP, Quad-core Core i7). All tests (‘ptestlong’) passed, on each system!

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
--

darwin doppelganger

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Jan 11, 2020, 6:24:42 PM1/11/20

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2017 MacBook Pro, 10.14.6,

make:

Sage build/upgrade complete!

make ptestlong:

----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 3997.5 seconds
cpu time: 18884.2 seconds
cumulative wall time: 30655.4 seconds

Jaap Spies

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Jan 12, 2020, 6:20:15 AM1/12/20

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All segmentation faults vanished! But new were introduced:

./sage -t --long src/sage/modular/btquotients/pautomorphicform.py # Timed out -> again

./sage -t --long src/sage/rings/finite_rings/residue_field.pyx # Timed out -> All tests passed

./sage -t --long src/sage/schemes/elliptic_curves/constructor.py # Timed out -> again

./sage -t --long src/sage/schemes/elliptic_curves/gal_reps.py # Timed out -> Segmentation fault!

./sage -t --long src/sage/schemes/elliptic_curves/ell_torsion.py # Timed out -> Segmentation fault

./sage -t --long src/sage/schemes/affine/affine_morphism.py # Timed out -> again

./sage -t --long src/sage/rings/morphism.pyx # Timed out -> Segmentation fault

I saved the output of:

bash failures > failure.log 2>&1 &

Anyone interested?

There were 3 'normal' test failures. Also present in sage-9.0. Ten days ago I made trac tickets: #28939, #28940 and #28941.

Eric Gourgoulhon

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Jan 13, 2020, 6:09:02 AM1/13/20

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

- build (with -j16) from a fresh git clone + pull develop: OK

- all tests from ptestlong passed

Eric

chris wuthrich

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Jan 14, 2020, 5:57:43 AM1/14/20

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make build after pulling 9.1.beta0 produces an error below. I have no problems compiling 9.0.

This is on centos 7 with devtoolset-4 enabled.

Sorry if this is noise produced by me making an error. Happy to provide any other information.

make -j4 build/make/Makefile --stop
make[1]: Entering directory `/local/pmzcw/prog/sage'
./bootstrap -d
make[2]: Entering directory `/local/pmzcw/prog/sage'
rm -rf config configure build/make/Makefile-auto.in
make[2]: Leaving directory `/local/pmzcw/prog/sage'
bootstrap:69: installing 'config/config.rpath'
configure.ac:113: installing 'config/config.guess'
configure.ac:113: installing 'config/config.sub'
configure.ac:68: installing 'config/install-sh'
configure.ac:68: installing 'config/missing'
configure.ac:453: error: possibly undefined macro: AC_CONFIG_COMMANDS
If this token and others are legitimate, please use m4_pattern_allow.
See the Autoconf documentation.
configure:10801: error: possibly undefined macro: PKG_CHECK_VAR
configure:10802: error: possibly undefined macro: AC_CONFIG_LINKS

configure:10807: error: possibly undefined macro: AC_MSG_WARN

make dist-clean also fails with

checking BLAS library... openblas

./configure: line 10801: syntax error near unexpected token `OPENBLASPCDIR,'
./configure: line 10801: ` PKG_CHECK_VAR(OPENBLASPCDIR, openblas, pcfiledir,'
If you would like to try to build Sage anyway (to help porting),
export the variable 'SAGE_PORT' to something non-empty.
make[1]: *** [build/make/Makefile] Error 1
make[1]: Leaving directory `/local/pmzcw/prog/sage'
make: *** [dist-clean] Error 2

Chris

Dima Pasechnik

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Jan 14, 2020, 6:24:57 AM1/14/20

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the latter is https://trac.sagemath.org/ticket/29001

(perhaps the former too, not sure)

>
>
> Chris
>
> --
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Dima Pasechnik

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Jan 14, 2020, 6:31:13 AM1/14/20

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On Tue, Jan 14, 2020 at 10:57 AM chris wuthrich
<christian...@gmail.com> wrote:
>
>
>

> make build after pulling 9.1.beta0 produces an error below. I have no problems compiling 9.0.
> This is on centos 7 with devtoolset-4 enabled.

https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/
says that devtoolset-4 is officially dead, since Dec 2017.

Can you move to something newer, e.g. devtoolset-7 ?

Markus Wageringel

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Jan 14, 2020, 12:58:43 PM1/14/20

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For now, `./bootstrap -D` can be used as a workaround for this problem.

> To unsubscribe from this group and stop receiving emails from it, send an email to sage-r...@googlegroups.com.

Martin R

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Jan 15, 2020, 4:12:14 AM1/15/20

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Dear all,

I have a problem with r-3.6.2 in 9.1.beta0 in an python2 build (incremental from a relatiively recent release, but I don't remember which) on Ubuntu 18.04.3, and I have absolutely no clue. The last bit of the error message is

[r-3.6.2] ../../Makeconf:124: recipe for target 'integrate.o' failed

[r-3.6.2] make[7]: *** [integrate.o] Error 1

sage starts and is otherwise usable.

The log is attached. It would be great if I could avoid rebuilding all of sage, because this is an old laptop...

Many many thanks,

Martin

r-3.6.2.log

Dima Pasechnik

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Jan 15, 2020, 4:19:35 AM1/15/20

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On Wed, Jan 15, 2020 at 9:12 AM 'Martin R' via sage-release
<sage-r...@googlegroups.com> wrote:
>
> Dear all,
>
> I have a problem with r-3.6.2 in 9.1.beta0 in an python2 build (incremental from a relatiively recent release, but I don't remember which) on Ubuntu 18.04.3, and I have absolutely no clue. The last bit of the error message is
>

The R problem is known, and related to recent gfortran releases.
https://developer.r-project.org/Blog/public/2019/05/15/gfortran-issues-with-lapack/

You might instead install openblas and R from the system, they should
be recognised.
(also gsl, cliquer, so, for Ubuntu, `apt-get libopenblas-dev
r-base-dev libgsl-dev libcliquer-dev cliquer`)
as well as `make openblas-clean gsl-clean cliquer-clean`
before ./configure && make build

> [r-3.6.2] ../../Makeconf:124: recipe for target 'integrate.o' failed
> [r-3.6.2] make[7]: *** [integrate.o] Error 1
>
> sage starts and is otherwise usable.
>
> The log is attached. It would be great if I could avoid rebuilding all of sage, because this is an old laptop...
>
> Many many thanks,
>
> Martin
>

> --
> 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...@googlegroups.com.
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chris wuthrich

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Jan 15, 2020, 4:36:51 AM1/15/20

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Thanks for the help.

I upgraded devtoolset to 7, but it is still pkg-config 0.27.1 there. So that didn't help.

Markus' suggestion solved it.

Chris

Martin R

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Jan 15, 2020, 5:01:16 AM1/15/20

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Many thanks for your help - unfortunately it didn't work though.

I am attaching the new config.log

Martin

Am Mittwoch, 15. Januar 2020 10:19:35 UTC+1 schrieb Dima Pasechnik:

On Wed, Jan 15, 2020 at 9:12 AM 'Martin R' via sage-release
<sage-r...@googlegroups.com> wrote:
>
> Dear all,
>

> I have a problem with r-3.6.2 in 9.1.beta0 in an python2 build (incremental from a relatiively recent release, but I don't remember which) on Ubuntu 18.04.3, and I have absolutely no clue. The last bit oortunatf the error message is

>
The R problem is known, and related to recent gfortran releases.
https://developer.r-project.org/Blog/public/2019/05/15/gfortran-issues-with-lapack/

You might instead install openblas and R from the system, they should
be recognised.
(also gsl, cliquer, so, for Ubuntu, `apt-get libopenblas-dev
r-base-dev libgsl-dev libcliquer-dev cliquer`)
as well as `make openblas-clean gsl-clean cliquer-clean`
before ./configure && make build

> [r-3.6.2] ../../Makeconf:124: recipe for target 'integrate.o' failed
> [r-3.6.2] make[7]: *** [integrate.o] Error 1
>
> sage starts and is otherwise usable.
>
> The log is attached. It would be great if I could avoid rebuilding all of sage, because this is an old laptop...
>
> Many many thanks,
>
> Martin
>
> --
> 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-r...@googlegroups.com.

config.log

Dima Pasechnik

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Jan 15, 2020, 5:13:09 AM1/15/20

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It seems you have remains of an old R installation in local/
So you need
rm -rf local/lib/R
rm local/bin/R*

and then re-run ./configure

(details ar in https://trac.sagemath.org/ticket/28884)

On Wed, Jan 15, 2020 at 10:01 AM 'Martin R' via sage-release

> To unsubscribe from this group and stop receiving emails from it, send an email to sage-release...@googlegroups.com.
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Martin R

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Jan 15, 2020, 5:37:11 AM1/15/20

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Thanks again! It still tries to build R and fails

I checked that system R starts, it does (R version 3.4.4)

The new config.log is attached.

Sorry and thank you!

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/a6968f7e-4e2f-49db-98a7-881d07d98b79%40googlegroups.com.

config.log

Dima Pasechnik

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Jan 15, 2020, 6:02:30 AM1/15/20

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On Wed, Jan 15, 2020 at 10:37 AM 'Martin R' via sage-release
<sage-r...@googlegroups.com> wrote:
>
> Thanks again! It still tries to build R and fails
>
> I checked that system R starts, it does (R version 3.4.4)

Please also make sure that

pkg-config --modversion libR

outputs the version.

However there is just no "checking for R" message in your config.log,
it indicates that there are still remains of R left
in your installation.

I've opened https://trac.sagemath.org/ticket/29016
to deal with R being hard to clean away - feel free to try it.

Maybe you also need to run

make r-clean

> To unsubscribe from this group and stop receiving emails from it, send an email to sage-release...@googlegroups.com.
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Martin R

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Jan 15, 2020, 6:35:27 AM1/15/20

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Am Mittwoch, 15. Januar 2020 12:02:30 UTC+1 schrieb Dima Pasechnik:

On Wed, Jan 15, 2020 at 10:37 AM 'Martin R' via sage-release
<sage-r...@googlegroups.com> wrote:
>
> Thanks again! It still tries to build R and fails
>
> I checked that system R starts, it does (R version 3.4.4)
Please also make sure that

pkg-config --modversion libR

outputs the version.

Yes, it does.

However there is just no "checking for R" message in your config.log,
it indicates that there are still remains of R left
in your installation.

I've opened https://trac.sagemath.org/ticket/29016
to deal with R being hard to clean away - feel free to try it.

Maybe you also need to run

make r-clean

I did that, it says that there is no legacy uninstaller for r, and that there is nothing to do. I checked for the files in the ticket, but none of them exists. :-(

The config.log contains the lines

configure:18950: checking installing any of atlas openblas iconv readline bzip2 xz pcre curl?

configure:18954: result: yes; install r as well

but I do not know how to find out which of those (atlas openblas iconv readline bzip2 xz pcre curl) is the problem.

Martin

Dima Pasechnik

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Jan 15, 2020, 7:00:51 AM1/15/20

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On Wed, Jan 15, 2020 at 11:35 AM 'Martin R' via sage-release

The easiest is to look at the output of ./configure
It should contain lines like

atlas-3.10.2.p3 will not be installed (configure check)

for each of the packages in that list.
So for any of these that are not marked this way, please install the
corresponding system package
and re-run configure.

>
> Martin
>
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Martin R

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Jan 15, 2020, 7:13:46 AM1/15/20

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Oh dea, this is becoming strange:

The output of configure says that

atlas, openblas, iconv will NOT be installed, but

bzip2-1.0.6-20150304.p0

readline-6.3.008.p0

xz-5.2.2.p0

pcre-8.40.p2

curl-7.62.0.p0

However, I certainly have bzip2, xz, pcre and curl on my system, and I guess also readline.

Might there be a bug in configure?

Martin

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Dima Pasechnik

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Jan 15, 2020, 7:23:17 AM1/15/20

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On Wed, Jan 15, 2020 at 12:13 PM 'Martin R' via sage-release
<sage-r...@googlegroups.com> wrote:
>
> Oh dea, this is becoming strange:
>
> The output of configure says that
>
> atlas, openblas, iconv will NOT be installed, but
>
> bzip2-1.0.6-20150304.p0
> readline-6.3.008.p0
> xz-5.2.2.p0
> pcre-8.40.p2
> curl-7.62.0.p0
>
> However, I certainly have bzip2, xz, pcre and curl on my system, and I guess also readline.
>
> Might there be a bug in configure?

You need development versions of these, see
https://doc.sagemath.org/html/en/installation/source.html#linux-recommended-installation

So, on Ubuntu:

libbz2-dev
libreadline-dev (seems to be missing in docs)
liblzma-dev (this is the xz lib, iirc)
libpcre3-dev
libcurl4-openssl-dev

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Martin R

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Jan 15, 2020, 7:53:45 AM1/15/20

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Am Mittwoch, 15. Januar 2020 13:23:17 UTC+1 schrieb Dima Pasechnik:

On Wed, Jan 15, 2020 at 12:13 PM 'Martin R' via sage-release
<sage-r...@googlegroups.com> wrote:
>
> Oh dea, this is becoming strange:
>
> The output of configure says that
>
> atlas, openblas, iconv will NOT be installed, but
>
> bzip2-1.0.6-20150304.p0
> readline-6.3.008.p0
> xz-5.2.2.p0
> pcre-8.40.p2
> curl-7.62.0.p0
>
> However, I certainly have bzip2, xz, pcre and curl on my system, and I guess also readline.
>
> Might there be a bug in configure?

You need development versions of these, see
https://doc.sagemath.org/html/en/installation/source.html#linux-recommended-installation

So, on Ubuntu:

libbz2-dev
libreadline-dev (seems to be missing in docs)
liblzma-dev (this is the xz lib, iirc)
libpcre3-dev
libcurl4-openssl-dev

the last of these, libcurl4-openssl-dev was indeed missing, but configure still wants to build r :-(

Martin

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Dima Pasechnik

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Jan 15, 2020, 8:00:29 AM1/15/20

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Note that you need to uninstall bzip2, xz, pcre, readline, curl before
the corresponding system
versions are picked up by ./configure (of course all this is not
needed for fresh builds...)

if this does not help please post config.log

On Wed, Jan 15, 2020 at 12:53 PM 'Martin R' via sage-release

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Martin R

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Jan 15, 2020, 8:07:49 AM1/15/20

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BINGO!!!

Many many many thanks!

Martin

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Martin R

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Jan 15, 2020, 8:16:39 AM1/15/20

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I'm afraid I was celebrating too early. make build succeeded, but sage doesn't start anymore now. I guess I should start from scratch. :-(

Martin R

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Jan 15, 2020, 8:18:20 AM1/15/20

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For the record:

ImportError: /usr/lib/x86_64-linux-gnu/libgsl.so.23: undefined symbol: cblas_ctrmv

Dima Pasechnik

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Jan 15, 2020, 8:22:50 AM1/15/20

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probably you need to rebuild at least sagelib.
./sage -f sagelib

On Wed, Jan 15, 2020 at 1:18 PM 'Martin R' via sage-release

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Emmanuel Charpentier

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Jan 15, 2020, 9:48:20 AM1/15/20

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On a slightly smaller machine (Debian testing, core i5, 8 GB RAM) with different installed software, an upgrade of 9.0 to 9.1.beta0 (Python 3-based) leads to ptestalllong getting 12 failures, all transient:

Using –optional=build,dochtml,dot2tex,external,fricas,giacpy_sage,libsemigroups,memlimit,python2,sage,sagenb
External software to be detected:
cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,scilab

File	Result	P/T
src/sage/plot/animate.py	7 doctests failed	T
src/sage/combinat/designs/ext_rep.py	2 doctests failed	T
src/sage/symbolic/integration/external.py	1 doctest failed	T
src/doc/en/constructions/linear_algebra.rst	1 doctest failed	T
src/sage/misc/latex.py	1 doctest failed	T
src/doc/en/constructions/interface_issues.rst	1 doctest failed	T
src/sage/databases/oeis.py	1 doctest failed	T
src/sage/repl/load.py	1 doctest failed	T
src/doc/en/developer/coding_in_other.rst	1 doctest failed	T
src/sage/interfaces/octave.py	3 doctests failed	T
src/sage/databases/findstat.py	8 doctests failed	T
src/sage/interfaces/magma_free.py	2 doctests failed	T

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

HTH,

Le samedi 11 janvier 2020 14:07:34 UTC+1, Emmanuel Charpentier a écrit :

On Debian testing running on core i7 + 16 GB RAM, upgrading a Python 3-based Sage 9.0 to 9.1.beta0 and running ptestalllong gets 3 permanent and 5 transient failures:

File Result P/T

src/sage/databases/oeis.py 1 doctest failed T

src/sage/plot/animate.py 7 doctests failed T

src/sage/numerical/backends/glpk_backend.pyx 1 doctest failed P

src/sage/tests/gap_packages.py 1 doctest failed P

src/sage/misc/latex.py 1 doctest failed T

src/sage/libs/glpk/error.pyx 1 doctest failed P

src/sage/repl/load.py 1 doctest failed T

src/sage/databases/findstat.py 8 doctests failed T

All of these failures have been reported multiple times. No new failure here.

HTH,

Sébastien Labbé

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Jan 20, 2020, 3:11:14 AM1/20/20

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I was late on this one, but let me post it for comparison purposes. Testing few 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/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 # Killed due to abort
sage -t --long src/sage/graphs/generators/smallgraphs.py # 2 doctests failed
sage -t --long src/sage/misc/latex.py # 1 doctest failed
sage -t --long src/sage/plot/animate.py # 7 doctests failed
sage -t --long src/sage/repl/load.py # 1 doctest 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 gives:

----------------------------------------------------------------------
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 # Killed due to abort
sage -t --long src/sage/graphs/generators/smallgraphs.py # 2 doctests failed
sage -t --long src/sage/misc/latex.py # 1 doctest failed
sage -t --long src/sage/plot/animate.py # 7 doctests failed
sage -t --long src/sage/repl/load.py # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,imagemagick,internet,latex

Follow up at: https://trac.sagemath.org/ticket/25536

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