[arch-commits] Commit in sagemath/repos/community-testing-x86_64 (17 files)

Antonio Rojas arojas at archlinux.org
Mon May 7 21:08:27 UTC 2018


    Date: Monday, May 7, 2018 @ 21:08:27
  Author: arojas
Revision: 319429

archrelease: copy trunk to community-testing-x86_64

Added:
  sagemath/repos/community-testing-x86_64/PKGBUILD
    (from rev 319428, sagemath/trunk/PKGBUILD)
  sagemath/repos/community-testing-x86_64/fes02.patch
    (from rev 319428, sagemath/trunk/fes02.patch)
  sagemath/repos/community-testing-x86_64/jupyter-path.patch
    (from rev 319428, sagemath/trunk/jupyter-path.patch)
  sagemath/repos/community-testing-x86_64/latte-count.patch
    (from rev 319428, sagemath/trunk/latte-count.patch)
  sagemath/repos/community-testing-x86_64/package.patch
    (from rev 319428, sagemath/trunk/package.patch)
  sagemath/repos/community-testing-x86_64/r-no-readline.patch
    (from rev 319428, sagemath/trunk/r-no-readline.patch)
  sagemath/repos/community-testing-x86_64/sagemath-detect-igraph.patch
    (from rev 319428, sagemath/trunk/sagemath-detect-igraph.patch)
  sagemath/repos/community-testing-x86_64/sagemath-env.patch
    (from rev 319428, sagemath/trunk/sagemath-env.patch)
  sagemath/repos/community-testing-x86_64/sagemath-ignore-warnings.patch
    (from rev 319428, sagemath/trunk/sagemath-ignore-warnings.patch)
  sagemath/repos/community-testing-x86_64/sagemath-lcalc-c++11.patch
    (from rev 319428, sagemath/trunk/sagemath-lcalc-c++11.patch)
  sagemath/repos/community-testing-x86_64/sagemath-lrs.patch
    (from rev 319428, sagemath/trunk/sagemath-lrs.patch)
  sagemath/repos/community-testing-x86_64/sagemath-networkx2.patch
    (from rev 319428, sagemath/trunk/sagemath-networkx2.patch)
  sagemath/repos/community-testing-x86_64/sagemath-python3-notebook.patch
    (from rev 319428, sagemath/trunk/sagemath-python3-notebook.patch)
  sagemath/repos/community-testing-x86_64/sagemath-scipy-1.0.patch
    (from rev 319428, sagemath/trunk/sagemath-scipy-1.0.patch)
  sagemath/repos/community-testing-x86_64/sagemath-singular-4.1.1.patch
    (from rev 319428, sagemath/trunk/sagemath-singular-4.1.1.patch)
  sagemath/repos/community-testing-x86_64/sagemath-threejs.patch
    (from rev 319428, sagemath/trunk/sagemath-threejs.patch)
  sagemath/repos/community-testing-x86_64/test-optional.patch
    (from rev 319428, sagemath/trunk/test-optional.patch)

---------------------------------+
 PKGBUILD                        |  170 ++++++++++++++++++++++++++++++++++++
 fes02.patch                     |   57 ++++++++++++
 jupyter-path.patch              |   22 ++++
 latte-count.patch               |   71 +++++++++++++++
 package.patch                   |   38 ++++++++
 r-no-readline.patch             |   11 ++
 sagemath-detect-igraph.patch    |   21 ++++
 sagemath-env.patch              |  149 ++++++++++++++++++++++++++++++++
 sagemath-ignore-warnings.patch  |   25 +++++
 sagemath-lcalc-c++11.patch      |   10 ++
 sagemath-lrs.patch              |   22 ++++
 sagemath-networkx2.patch        |  175 ++++++++++++++++++++++++++++++++++++++
 sagemath-python3-notebook.patch |   27 +++++
 sagemath-scipy-1.0.patch        |   16 +++
 sagemath-singular-4.1.1.patch   |   94 ++++++++++++++++++++
 sagemath-threejs.patch          |   11 ++
 test-optional.patch             |   27 +++++
 17 files changed, 946 insertions(+)

Copied: sagemath/repos/community-testing-x86_64/PKGBUILD (from rev 319428, sagemath/trunk/PKGBUILD)
===================================================================
--- PKGBUILD	                        (rev 0)
+++ PKGBUILD	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,170 @@
+# Maintainer: Antonio Rojas <arojas at archlinux.org>
+# Contributor: Evgeniy Alekseev <arcanis.arch at gmail dot com>
+# Contributor: Daniel Wallace <danielwallace at gtmanfred dot com>
+# Contributor: Thomas Dziedzic <gostrc at gmail dot com>
+# Contributor: Osman Ugus <ugus11 at yahoo dot com>
+# Contributor: Stefan Husmann <stefan-husmann at t-online dot de>
+# Special thanks to Nareto for moving the compile from the .install to the PKGBUILD
+
+pkgbase=sagemath
+pkgname=(sagemath sagemath-jupyter)
+pkgver=8.2
+pkgrel=2
+pkgdesc="Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"
+arch=(x86_64)
+url="http://www.sagemath.org"
+license=(GPL)
+depends=(ipython2 ppl palp brial cliquer maxima-ecl gfan sympow nauty python2-rpy2 python2-fpylll python2-psutil python2-cypari2
+  python2-matplotlib python2-scipy python2-sympy python2-networkx python2-pillow python2-future libgap flintqs lcalc lrcalc arb
+  eclib gmp-ecm zn_poly gd python2-cvxopt pynac linbox rubiks pari-galdata pari-seadata-small planarity rankwidth tachyon
+  sage-data-combinatorial_designs sage-data-elliptic_curves sage-data-graphs sage-data-polytopes_db sage-data-conway_polynomials)
+optdepends=('cython2: to compile cython code' 'python2-pkgconfig: to compile cython code'
+  'jmol: 3D plots' 'sage-notebook: Flask notebook interface (deprecated)'
+  'sagemath-doc: Documentation and inline help' 'python2-igraph: igraph backend for graph theory'
+  'coin-or-cbc: COIN backend for numerical computations' 'coin-or-csdp: for computing Lovász theta-function of graphs'
+  'buckygen: for generating fullerene graphs' 'plantri: for generating some classes of graphs' 'benzene: for generating fusenes and benzenoids'
+  'ffmpeg: to export animations to video' 'imagemagick: to show animations'
+  'coxeter: Coxeter groups implementation' 'cryptominisat5: SAT solver' 'gap-data: for computing Galois groups'
+  'lrs: Algorithms for linear reverse search used in game theory and for computing volume of polytopes'
+  'libhomfly: for computing the homfly polynomial of links' 'libbraiding: for computing in braid groups'
+  'libfes: exhaustive search of solutions for boolean equations' 'python2-pynormaliz: Normaliz backend for polyhedral computations'
+  'latte-integrale: integral point count in polyhedra' 'polymake: polymake backend for polyhedral computations'
+  'shared_meataxe: faster matrix arithmetic over finite fields'
+  'sirocco: for computing the fundamental group of the complement of a plane curve'
+  'three.js: alternative 3D plots engine')
+makedepends=(cython2 boost ratpoints symmetrica python2-jinja coin-or-cbc libhomfly libbraiding sirocco
+  mcqd coxeter bliss-graphs tdlib python2-pkgconfig shared_meataxe libfes)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/sagemath/sage/archive/$pkgver.tar.gz"
+        sagemath-env.patch package.patch latte-count.patch jupyter-path.patch sagemath-python3-notebook.patch test-optional.patch
+        r-no-readline.patch fes02.patch sagemath-threejs.patch sagemath-ignore-warnings.patch
+        sagemath-detect-igraph.patch sagemath-networkx2.patch sagemath-scipy-1.0.patch sagemath-lrs.patch
+        sagemath-singular-4.1.1.patch sagemath-lcalc-c++11.patch
+        pari-ratpoints.patch::"https://github.com/sagemath/sage/commit/83458400.patch")
+sha256sums=('41ba2c2dde7a02e1bb6880ae875d37ab058567cc26e760efe87eeb12188cd65b'
+            '6f95ef6960acb3b368bc6245783d88fcadaa63537e1bf9f41d8d91b28e95ddf9'
+            'c41ae665499c6cd775d40bbe178f8786830b0931ee26bf11ee02f7d83bcc8107'
+            '0b680e674c11c47afa86162d8b49645620b8912722e08133d23357c29ca9310a'
+            '2cad308f8adbb6c54e6603fa22b2f0eb60f6f09248d5d015000c3932ac14f646'
+            '962ce805c87147212b21fc2ab0ac9af9bd0033942c7a6905b9906645b48e8a4f'
+            '18edeafb01cc1ed7270c2dfb41a58717918680c98e8eada1858736acd65d92ba'
+            'afd0952b9bb8f52fd428eae36cf719a58ff85a894baae88cbb2124e043768cc7'
+            '7fcb52e96935dccb0f958d37c2f4e3918392480b9af53e08562f6cba6c68cb94'
+            '2d13b15ad2d1511bb3d752a261497060a8901882b1c2fa9813219781b7a71d83'
+            'a4a6c87b46ff23b89608aca66d00427334502e8bfb5dfe68b94497d19be1c7ae'
+            'bfe49f0168fe0824f0eaf4ea793b08d5b3e43c4e3634eb5f664c70644a793a59'
+            '8253730940687992dd29d90d95bea7e2685bb4854db004090c8196ce92859b64'
+            '17397b8e1843b013ef5d2e083369109f0719651edd8ef0c8493cb49e2bc4324a'
+            'c0f65534a845ba802de6196229159fe67fcc3f72f0cb1ce57d4ae5c9fe10282c'
+            '369f1483e0364031d73d43d9e63b7bf2b0929c8a1d470c1596f98f9f1aa80750'
+            '5114c912f821900e5bfae1e2cfeb7984de946d0b23e1182b0bf15be1d803dfd0'
+            'e24ad879f6b2eb970778fc5e867bcbe0a6d393feca8f11f5cb8d07da1f024be9')
+
+prepare(){
+  cd sage-$pkgver
+
+# Arch-specific patches
+# assume all optional packages are installed
+  patch -p0 -i ../package.patch
+# set env variables
+  patch -p0 -i ../sagemath-env.patch
+# don't list optional packages when running tests
+  patch -p0 -i ../test-optional.patch
+# set jupyter path
+  patch -p0 -i ../jupyter-path.patch
+# fix freezes in R interface with readline 7 (Debian)
+  patch -p1 -i ../r-no-readline.patch
+# use correct latte-count binary name
+  patch -p1 -i ../latte-count.patch
+# make 'sage -notebook=jupyter' work with our python3 jupyter-notebook package
+  patch -p1 -i ../sagemath-python3-notebook.patch
+# fix Cremona database detection
+  sed -e "s|is_package_installed('database_cremona_ellcurve')|os.path.exists('/usr/share/cremona/cremona.db')|" \
+   -i src/sage/databases/cremona.py
+# fix python-igraph detection
+  patch -p1 -i ../sagemath-detect-igraph.patch
+# fix lrs detection
+  patch -p1 -i ../sagemath-lrs.patch
+# adapt to networkx 2 changes
+  patch -p1 -i ../sagemath-networkx2.patch
+# fix three.js plotting backend
+  patch -p1 -i ../sagemath-threejs.patch
+# don't show PARI stack size increase or GLPK warnings during doctesting (Debian)
+  patch -p1 -i ../sagemath-ignore-warnings.patch
+# remove deprecated scipy parameters
+  patch -p1 -i ../sagemath-scipy-1.0.patch
+# fix build with Singular 4.1.1
+  patch -p1 -i ../sagemath-singular-4.1.1.patch
+# revert usage of development PARI features
+  patch -Rp1 -i ../pari-ratpoints.patch
+# don't force c++98 for lcalc (fixes build with NTL 11)
+  patch -p1 -i ../sagemath-lcalc-c++11.patch
+
+# Upstream patches  
+# fix build against libfes 0.2 http://trac.sagemath.org/ticket/15209
+  patch -p1 -i ../fes02.patch
+
+# use python2
+  sed -e 's|#!/usr/bin/env sage-python23|#!/usr/bin/env python2|' -e 's|\<#!/usr/bin/env sage-python\>|#!/usr/bin/env python2|' \
+    -e 's|\<exec python\>|exec python2|' -i src/bin/*
+  sed -e 's|cython {OPT}|cython2 {OPT}|' -e 's|python setup.py|python2 setup.py|' -i src/sage/misc/cython.py
+  sed -e 's|exec ipython|exec ipython2|' -e 's|cygdb|cygdb2|g' -i src/bin/sage
+  sed -e "s|'cython'|'cython2'|" -i src/bin/sage-cython
+  sed -e 's|bin/python|bin/python2|g' -i src/bin/sage-env
+}
+
+
+build() {
+  cd sage-$pkgver/src
+
+  export SAGE_ROOT="$PWD"
+  export SAGE_SRC="$PWD"
+  python2 setup.py build
+}
+
+package_sagemath() {
+  optdepends+=('sagemath-jupyter: Jupyter kernel')
+
+  cd sage-$pkgver/src
+
+  export SAGE_ROOT="$PWD"
+  export SAGE_LOCAL="/usr"
+  export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+  python2 setup.py install --root="$pkgdir" --optimize=1
+
+  mkdir -p "$pkgdir"/usr/bin
+  cp bin/sage "$pkgdir"/usr/bin
+  for _i in arch-env cachegrind callgrind cleaner coverage coverageall cython env eval grep grepdoc inline-fortran \
+    ipython massif maxima.lisp native-execute notebook num-threads.py omega open preparse python rst2sws rst2txt run \
+    run-cython runtests startuptime.py sws2rst valgrind version.sh
+  do
+    cp bin/sage-$_i "$pkgdir"/usr/bin
+  done
+  cp bin/math-readline "$pkgdir"/usr/bin
+  
+  mkdir -p "$pkgdir"/usr/share/sage
+  cp -r ext "$pkgdir"/usr/share/sage
+  
+# Create SAGE_SRC, needed for the notebook and help
+  mkdir "$pkgdir"/usr/share/sage/source
+  ln -s /usr/share/doc/sage "$pkgdir"/usr/share/sage/source/doc
+
+# Remove sage_setup
+  rm -r "$pkgdir"/usr/lib/python2.7/site-packages/sage_setup
+
+# Split jupyter kernel
+  rm -r "$pkgdir"/usr/share/jupyter
+}
+
+package_sagemath-jupyter() {
+  pkgdesc='Jupyter kernel for SageMath'
+  depends=(sagemath python2-jupyter_client python2-ipywidgets mathjax)
+  optdepends=('sage-notebook-exporter: convert flask notebooks to Jupyter')
+
+  cd sage-$pkgver/src
+
+  export SAGE_ROOT="$PWD"
+  export SAGE_LOCAL="/usr"
+  export JUPYTER_PATH="$pkgdir"/usr/share/jupyter
+
+  python2 -c "from sage.repl.ipython_kernel.install import SageKernelSpec; SageKernelSpec.update()"
+}

Copied: sagemath/repos/community-testing-x86_64/fes02.patch (from rev 319428, sagemath/trunk/fes02.patch)
===================================================================
--- fes02.patch	                        (rev 0)
+++ fes02.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,57 @@
+From b1f5e3ecc789db674fe17552812f2d0e2ab84be0 Mon Sep 17 00:00:00 2001
+From: Charles Bouillaguet <charles.bouillaguet at lifl.fr>
+Date: Thu, 19 Sep 2013 10:31:11 +0200
+Subject: updating the libFES binding to match a change in the interface
+
+---
+ src/sage/libs/fes.pyx | 12 +++++++-----
+ 1 file changed, 7 insertions(+), 5 deletions(-)
+
+diff --git a/src/sage/libs/fes.pyx b/src/sage/libs/fes.pyx
+index 40b9c23..d188cf0 100644
+--- a/src/sage/libs/fes.pyx
++++ b/src/sage/libs/fes.pyx
+@@ -1,17 +1,19 @@
+ """
+-Binding for the FES library.
++Binding for the libFES library.
+ 
+ Finding solutions of systems of boolean equations by exhaustive
+ search, via the fes library. This is usually (much) faster than
+ computing a Groebner basis, except in special cases where the latter
+ is particularly easy.
+ 
+-The FES library is presently only able to deal with polynomials in 64
++More information is available at [http://www.lifl.fr/~bouillag/fes].
++
++The libFES library is presently only able to deal with polynomials in 64
+ variables. Performing a full exhaustive search over 64 variables will
+ take a **long** time. The number of variables can be artificially
+ reduced to 64 by specializing some of them.
+ 
+-Note that the FES library **requires** at least of the equations to be
++Note that the libFES library **requires** at least of the equations to be
+ non-linear.
+ 
+ AUTHORS:
+@@ -71,7 +73,7 @@ from libc.stdint cimport uint64_t
+ cdef extern from "fes_interface.h":
+     ctypedef int (*solution_callback_t)(void *, uint64_t)
+ 
+-    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose)
++    void exhaustive_search_wrapper(int n, int n_eqs, int degree, int ***coeffs, solution_callback_t callback, void* callback_state, int verbose, int T)
+ 
+ 
+ from sage.rings.integer import Integer
+@@ -217,7 +217,7 @@ def exhaustive_search(eqs,  max_sols=Infinity, verbose=False):
+ 
+     # ------- runs the library
+     sig_on()
+-    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose)
++    exhaustive_search_wrapper(n, len(eqs), degree, coeffs, report_solution, <void *> internal_state, verbose, 0)
+     sig_off()
+ 
+     # ------- frees memory occupied by the dense representation of the equations
+-- 
+cgit v1.0-1-gd88e
+

Copied: sagemath/repos/community-testing-x86_64/jupyter-path.patch (from rev 319428, sagemath/trunk/jupyter-path.patch)
===================================================================
--- jupyter-path.patch	                        (rev 0)
+++ jupyter-path.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,22 @@
+--- src/sage/repl/ipython_kernel/install.py.orig	2015-10-23 19:23:39.728456590 +0000
++++ src/sage/repl/ipython_kernel/install.py	2015-10-23 19:24:00.965018978 +0000
+@@ -13,8 +13,7 @@
+     SAGE_DOC, SAGE_LOCAL, SAGE_EXTCODE,
+     SAGE_VERSION
+ )
+-from jupyter_core.paths import ENV_JUPYTER_PATH
+-JUPYTER_PATH = ENV_JUPYTER_PATH[0]
++JUPYTER_PATH = os.environ.get('JUPYTER_PATH') 
+ 
+ 
+ class SageKernelSpec(object):
+@@ -225,7 +225,7 @@
+             sage: spec._symlink_resources()    # not tested
+         """
+         path = os.path.join(SAGE_EXTCODE, 'notebook-ipython')
+-        for filename in os.listdir(path):
++        for filename in os.listdir('ext/notebook-ipython'):
+             self.symlink(
+                 os.path.join(path, filename),
+                 os.path.join(self.kernel_dir, filename)
+

Copied: sagemath/repos/community-testing-x86_64/latte-count.patch (from rev 319428, sagemath/trunk/latte-count.patch)
===================================================================
--- latte-count.patch	                        (rev 0)
+++ latte-count.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,71 @@
+diff --git a/src/sage/geometry/polyhedron/base_ZZ.py b/src/sage/geometry/polyhedron/base_ZZ.py
+index 268af9db0d..70d41dfa30 100644
+--- a/src/sage/geometry/polyhedron/base_ZZ.py
++++ b/src/sage/geometry/polyhedron/base_ZZ.py
+@@ -171,7 +171,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(maxdet=5, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--maxdet=5' /dev/stdin
+             ...
+             sage: p    # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -179,7 +179,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(dual=True, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --dual /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -187,7 +187,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(irrational_primal=True, verbose=True)   # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-primal /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -195,7 +195,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             sage: p = P.ehrhart_polynomial(irrational_all_primal=True, verbose=True)  # optional - latte_int
+             This is LattE integrale ...
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd --irrational-all-primal /dev/stdin
+             ...
+             sage: p   # optional - latte_int
+             1/2*t^2 + 3/2*t + 1
+@@ -207,7 +207,7 @@ class Polyhedron_ZZ(Polyhedron_base):
+             ...
+             RuntimeError: LattE integrale program failed (exit code 1):
+             ...
+-            Invocation: count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
++            Invocation: latte-count --ehrhart-polynomial '--redundancy-check=none' --cdd '--bim-bam-boum=19' /dev/stdin
+             Unknown command/option --bim-bam-boum=19
+         """
+         if self.is_empty():
+diff --git a/src/sage/interfaces/latte.py b/src/sage/interfaces/latte.py
+index 066cedd401..302b39910d 100644
+--- a/src/sage/interfaces/latte.py
++++ b/src/sage/interfaces/latte.py
+@@ -88,7 +88,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
+         sage: n = count(cddin, cdd=True, verbose=True, raw_output=True)  # optional - latte_int
+         This is LattE integrale ...
+         ...
+-        Invocation: count '--redundancy-check=none' --cdd /dev/stdin
++        Invocation: latte-count '--redundancy-check=none' --cdd /dev/stdin
+         ...
+         Total Unimodular Cones: ...
+         Maximum number of simplicial cones in memory at once: ...
+@@ -108,7 +108,7 @@ def count(arg, ehrhart_polynomial=False, multivariate_generating_function=False,
+     from sage.misc.misc import SAGE_TMP
+     from sage.rings.integer import Integer
+ 
+-    args = ['count']
++    args = ['latte-count']
+     if ehrhart_polynomial and multivariate_generating_function:
+         raise ValueError
+     if ehrhart_polynomial:

Copied: sagemath/repos/community-testing-x86_64/package.patch (from rev 319428, sagemath/trunk/package.patch)
===================================================================
--- package.patch	                        (rev 0)
+++ package.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,38 @@
+--- src/sage/misc/package.py.orig	2014-11-23 15:58:13.000000000 +0100
++++ src/sage/misc/package.py	2015-01-22 20:32:25.651383902 +0100
+@@ -320,7 +320,7 @@
+         sage: for pkg in list_packages('pip', local=True):
+         ....:     assert not is_package_installed(pkg)
+     """
+-    return any(p.split('-')[0] == package for p in installed_packages(exclude_pip))
++    return True
+ 
+ def package_versions(package_type, local=False):
+     r"""
+--- src/sage_setup/optional_extension.py.orig  2016-10-19 18:35:10.092577510 +0000
++++ src/sage_setup/optional_extension.py       2016-10-19 18:38:13.514765366 +0000
+@@ -21,8 +21,6 @@
+ from distutils.extension import Extension
+ from sage.misc.package import is_package_installed, list_packages
+ 
+-all_packages = list_packages(local=True)
+-
+ 
+ class CythonizeExtension(Extension):
+     """
+@@ -76,14 +74,7 @@
+         condition = kwds.pop("condition")
+     except KeyError:
+         pkg = kwds.pop("package")
+-        try:
+-            pkginfo = all_packages[pkg]
+-        except KeyError:
+-            # Might be an installed old-style package
+-            condition = is_package_installed(pkg)
+-        else:
+-            condition = (pkginfo["installed_version"] == pkginfo["remote_version"])
+-
++        condition = True
+     if condition:
+         return Extension(*args, **kwds)
+     else:

Copied: sagemath/repos/community-testing-x86_64/r-no-readline.patch (from rev 319428, sagemath/trunk/r-no-readline.patch)
===================================================================
--- r-no-readline.patch	                        (rev 0)
+++ r-no-readline.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,11 @@
+--- a/src/sage/interfaces/r.py
++++ b/src/sage/interfaces/r.py
+@@ -332,7 +332,7 @@
+                   prompt = '> ', #default, later comes the change
+ 
+                   # This is the command that starts up your program
+-                  command = "R --vanilla --quiet",
++                  command = "R --no-readline --vanilla --quiet",
+ 
+                   server=server,
+                   server_tmpdir=server_tmpdir,

Copied: sagemath/repos/community-testing-x86_64/sagemath-detect-igraph.patch (from rev 319428, sagemath/trunk/sagemath-detect-igraph.patch)
===================================================================
--- sagemath-detect-igraph.patch	                        (rev 0)
+++ sagemath-detect-igraph.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,21 @@
+diff --git a/src/sage/graphs/generic_graph.py b/src/sage/graphs/generic_graph.py
+index 252984f..ce19682 100644
+--- a/src/sage/graphs/generic_graph.py
++++ b/src/sage/graphs/generic_graph.py
+@@ -8480,10 +8480,12 @@ class GenericGraph(GenericGraph_pyx):
+         if algorithm is None:
+             if vertex_bound:
+                 algorithm = "LP"
+-            elif is_package_installed("python_igraph"):
+-                algorithm = "igraph"
+             else:
+-                algorithm = "FF"
++                algorithm = "igraph"
++                try:
++                    import igraph
++                except ImportError:
++                    algorithm = "FF"
+ 
+         if (algorithm == "FF"):
+             return self._ford_fulkerson(x,y, value_only=value_only, integer=integer, use_edge_labels=use_edge_labels)
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-env.patch (from rev 319428, sagemath/trunk/sagemath-env.patch)
===================================================================
--- sagemath-env.patch	                        (rev 0)
+++ sagemath-env.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,149 @@
+--- src/bin/sage-env.orig	2015-01-06 10:46:04.469687605 +0100
++++ src/bin/sage-env	2015-01-06 10:49:59.547762019 +0100
+@@ -111,41 +111,7 @@
+ }
+ 
+ 
+-# New value for SAGE_ROOT: either SAGE_ROOT (if given)
+-# or a guessed value based on pwd.
+-if [ -n "$SAGE_ROOT" ]; then
+-    NEW_SAGE_ROOT="$SAGE_ROOT"
+-elif [ -f sage -a -d build ]; then
+-    NEW_SAGE_ROOT="."
+-elif [ -f ../../sage -a -d ../../build ]; then
+-    NEW_SAGE_ROOT="../.."
+-else
+-    # No idea what SAGE_ROOT should be...
+-    echo >&2 "Error: You must set the SAGE_ROOT environment variable or run this"
+-    echo >&2 "script from the SAGE_ROOT or SAGE_ROOT/local/bin/ directory."
+-    return 1
+-fi
+-
+-# Make NEW_SAGE_ROOT absolute
+-NEW_SAGE_ROOT=`cd "$NEW_SAGE_ROOT" && pwd -P`
+-
+-# Sanity check NEW_SAGE_ROOT
+-if [ -f "$NEW_SAGE_ROOT/sage" -a -d "$NEW_SAGE_ROOT/build" ]; then
+-    :
+-else
+-    echo >&2 "Error: SAGE_ROOT is set to a bad value:"
+-    echo >&2 "SAGE_ROOT=$SAGE_ROOT"
+-    echo >&2 "You must correct it or erase it and run this script from the SAGE_ROOT"
+-    echo >&2 "or SAGE_ROOT/local/bin/ directory."
+-    return 1
+-fi
+-
+-# Warn if NEW_SAGE_ROOT does not equal the old SAGE_ROOT
+-if [ "$SAGE_ROOT" != "$NEW_SAGE_ROOT" -a -n "$SAGE_ROOT" ]; then
+-    echo >&2 "Warning: overwriting SAGE_ROOT environment variable:"
+-    echo >&2 "Old SAGE_ROOT=$SAGE_ROOT"
+-    echo >&2 "New SAGE_ROOT=$NEW_SAGE_ROOT"
+-fi
++NEW_SAGE_ROOT="/usr"
+ 
+ 
+ # Don't execute the commands more than once for the same version of
+@@ -174,33 +174,9 @@
+ export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION
+ 
+ export SAGE_ROOT="$NEW_SAGE_ROOT"
++export SAGE_LOCAL='/usr'
++export SAGE_SCRIPTS_DIR='/usr/bin'
+ 
+-
+-# sage-env must know where the Sage's script files are.
+-# Note that SAGE_SCRIPTS_DIR is only used here, so it does not need to
+-# be exported.
+-if [ -z "$SAGE_SCRIPTS_DIR" ]; then
+-    if [ -n "$SAGE_LOCAL" ] && [ -f "$SAGE_LOCAL/bin/sage-env-config" ]; then
+-        SAGE_SCRIPTS_DIR="$SAGE_LOCAL/bin"
+-    elif [ -f "$SAGE_ROOT/src/bin/sage-env-config" ]; then
+-        SAGE_SCRIPTS_DIR="$SAGE_ROOT/src/bin"
+-    else
+-        echo >&2 "Error: You must set either the SAGE_LOCAL or SAGE_SCRIPTS_DIR environment variable to run this"
+-        return 1
+-    fi
+-elif [ ! -f "$SAGE_SCRIPTS_DIR/sage-env-config" ]; then
+-    echo >&2 "Error: SAGE_SCRIPTS_DIR is set to a bad value:"
+-    echo >&2 "SAGE_SCRIPTS_DIR=$SAGE_SCRIPTS_DIR"
+-    echo >&2 "You must correct it or erase it and rerun this script"
+-    return 1
+-fi
+-
+-# Set environment variables (like SAGE_LOCAL) depending on ./configure
+-. "$SAGE_SCRIPTS_DIR/sage-env-config"
+-if [ $? -ne 0 ]; then
+-    echo >&2 "Error: failed to source $SAGE_SCRIPTS_DIR/sage-env-config"
+-    return 1
+-fi
+ 
+ # The compilers are set in order of priority by
+ # 1) environment variables
+@@ -296,8 +296,9 @@
+ export SAGE_EXTCODE="$SAGE_SHARE/sage/ext"
+ export SAGE_SPKG_INST="$SAGE_LOCAL/var/lib/sage/installed"
+ export SAGE_LOGS="$SAGE_ROOT/logs/pkgs"
+-export SAGE_SRC="$SAGE_ROOT/src"
+-export SAGE_DOC_SRC="$SAGE_SRC/doc"
++export GAP_ROOT_DIR="/usr/lib/gap"
++export SAGE_SRC="$SAGE_LOCAL/lib/python2.7/site-packages"
++export SAGE_DOC_SRC="$SAGE_SHARE/doc/sage"
+ export SAGE_DOC="$SAGE_SHARE/doc/sage"
+ 
+ if [ -z "${SAGE_ORIG_PATH_SET}" ]; then
+@@ -403,6 +403,9 @@
+     export SAGE_STARTUP_FILE
+ fi
+ 
++export LIBMTX="$DOT_SAGE/meataxe"
++[[ -d $LIBMTX ]] || mkdir -p $LIBMTX # Create meataxe data dir
++
+ if [ "$PYTHON_EGG_CACHE" = "" ]; then
+     PYTHON_EGG_CACHE="$DOT_SAGE/.python-eggs"
+     export PYTHON_EGG_CACHE
+@@ -488,7 +488,6 @@
+         fi
+     fi
+ fi
+-export MAXIMA_PREFIX="$SAGE_LOCAL"
+ 
+ PERL5LIB="$SAGE_LOCAL/lib/perl5:$PERL5LIB" && export PERL5LIB
+ 
+@@ -608,9 +608,6 @@
+     LD_LIBRARY_PATH="$SAGE_LOCAL/bin:$LD_LIBRARY_PATH" && export LD_LIBRARY_PATH
+ fi
+ 
+-# See trac 7186 -- this is needed if ecl is moved
+-ECLDIR="$SAGE_LOCAL/lib/ecl/" && export ECLDIR
+-
+ # Handle parallel building/testing/...
+ # See Trac Ticket #12016
+ # First, figure out the right values for SAGE_NUM_THREADS (default
+--- src/sage/env.py.orig       2017-12-07 19:51:25.554281539 +0000
++++ src/sage/env.py    2017-12-07 19:51:42.787654650 +0000
+@@ -117,13 +117,13 @@
+ _add_variable_or_fallback('LOCAL_IDENTIFIER','$HOSTNAME.%s'%os.getpid())
+ 
+ # bunch of sage directories and files
+-_add_variable_or_fallback('SAGE_ROOT',       None)
+-_add_variable_or_fallback('SAGE_LOCAL',      None)
++_add_variable_or_fallback('SAGE_ROOT',       '')
++_add_variable_or_fallback('SAGE_LOCAL',      '/usr')
+ _add_variable_or_fallback('SAGE_ETC',        opj('$SAGE_LOCAL', 'etc'))
+ _add_variable_or_fallback('SAGE_INC',        opj('$SAGE_LOCAL', 'include'))
+ _add_variable_or_fallback('SAGE_SHARE',      opj('$SAGE_LOCAL', 'share'))
+ 
+-_add_variable_or_fallback('SAGE_SRC',        opj('$SAGE_ROOT', 'src'))
++_add_variable_or_fallback('SAGE_SRC',        opj('$SAGE_LOCAL', 'lib', 'python2.7', 'site-packages'))
+ 
+ try:
+     sitepackages_dirs = site.getsitepackages()
+@@ -163,7 +163,7 @@
+ _add_variable_or_fallback('GRAPHS_DATA_DIR',  opj('$SAGE_SHARE','graphs'))
+ _add_variable_or_fallback('ELLCURVE_DATA_DIR',opj('$SAGE_SHARE','ellcurves'))
+ _add_variable_or_fallback('POLYTOPE_DATA_DIR',opj('$SAGE_SHARE','reflexive_polytopes'))
+-_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_LOCAL','gap','latest'))
++_add_variable_or_fallback('GAP_ROOT_DIR',     opj('$SAGE_LOCAL','lib','gap'))
+ _add_variable_or_fallback('THEBE_DIR',        opj('$SAGE_SHARE','thebe'))
+ 
+ # locate singular shared object

Copied: sagemath/repos/community-testing-x86_64/sagemath-ignore-warnings.patch (from rev 319428, sagemath/trunk/sagemath-ignore-warnings.patch)
===================================================================
--- sagemath-ignore-warnings.patch	                        (rev 0)
+++ sagemath-ignore-warnings.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,25 @@
+Description: Ignore warnings of PARI increasing the stack size when parsing doctests
+ Since we can't patch PARI to not produce the warnings and we don't want to
+ patch tons of doctests to expect the warnings, we patch the doctest parser
+ to ignore them.
+Author: Tobias Hansen <thansen at debian.org>
+--- sage/src/sage/doctest/parsing.py
++++ sage/src/sage/doctest/parsing.py
+@@ -40,6 +40,8 @@
+ 
+ float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)')
+ optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
++pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.')
++glpk_simplex_warning_regex = re.compile(r'(Long-step dual simplex will be used)')
+ find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
+ find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
+ random_marker = re.compile('.*random', re.I)
+@@ -935,6 +936,8 @@
+             <type 'float'>
+         """
+         got = self.human_readable_escape_sequences(got)
++        got = pari_stack_warning_regex.sub('', got)
++        got = glpk_simplex_warning_regex.sub('', got)
+         if isinstance(want, MarkedOutput):
+             if want.random:
+                 return True

Copied: sagemath/repos/community-testing-x86_64/sagemath-lcalc-c++11.patch (from rev 319428, sagemath/trunk/sagemath-lcalc-c++11.patch)
===================================================================
--- sagemath-lcalc-c++11.patch	                        (rev 0)
+++ sagemath-lcalc-c++11.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,10 @@
+--- a/src/sage/libs/lcalc/lcalc_Lfunction.pxd
++++ b/src/sage/libs/lcalc/lcalc_Lfunction.pxd
+@@ -1,6 +1,5 @@
+ # Lcalc requires GNU extensions, it does not strictly conform to any
+ # C++ standard: https://trac.sagemath.org/ticket/23341
+-# distutils: extra_compile_args = -std=gnu++98
+ 
+ cdef extern from "lcalc_sage.h":
+     ctypedef struct doublevec "std::vector<double>":
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-lrs.patch (from rev 319428, sagemath/trunk/sagemath-lrs.patch)
===================================================================
--- sagemath-lrs.patch	                        (rev 0)
+++ sagemath-lrs.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,22 @@
+diff --git a/src/sage/game_theory/normal_form_game.py b/src/sage/game_theory/normal_form_game.py
+index 2115de6800..da94aa5d45 100644
+--- a/src/sage/game_theory/normal_form_game.py
++++ b/src/sage/game_theory/normal_form_game.py
+@@ -621,6 +621,7 @@ from sage.matrix.constructor import vector
+ from sage.misc.package import is_package_installed, PackageNotFoundError
+ from sage.misc.temporary_file import tmp_filename
+ from sage.numerical.mip import MixedIntegerLinearProgram
++import os
+ 
+ try:
+     from gambit import Game
+@@ -1636,7 +1637,7 @@ class NormalFormGame(SageObject, MutableMapping):
+         if not algorithm:
+             if self.is_constant_sum():
+                 algorithm = "lp"
+-            elif is_package_installed('lrslib'):
++            elif os.path.exists('/usr/bin/lrsnash'):
+                 algorithm = "lrs"
+             else:
+                 algorithm = "enumeration"
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-networkx2.patch (from rev 319428, sagemath/trunk/sagemath-networkx2.patch)
===================================================================
--- sagemath-networkx2.patch	                        (rev 0)
+++ sagemath-networkx2.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,175 @@
+diff --git a/src/sage/graphs/base/graph_backends.pyx b/src/sage/graphs/base/graph_backends.pyx
+index ff1d02900a..bad4a18539 100644
+--- a/src/sage/graphs/base/graph_backends.pyx
++++ b/src/sage/graphs/base/graph_backends.pyx
+@@ -800,9 +800,9 @@ class NetworkXGraphDeprecated(SageObject):
+             sage: X.multiedges = True
+             sage: G = X.mutate()
+             sage: G.edges()
+-            [(1, 2), (2, 3)]
++            MultiEdgeDataView([(1, 2), (2, 3)])
+             sage: G.edges(data=True)
+-            [(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]
++            MultiEdgeDataView([(1, 2, {'weight': 7}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})])
+ 
+         """
+         import networkx
+@@ -868,11 +868,9 @@ class NetworkXDiGraphDeprecated(SageObject):
+             sage: X.multiedges = True
+             sage: G = X.mutate()
+             sage: G.edges()
+-            [(1, 2), (2, 1), (2, 3)]
++            OutMultiEdgeDataView([(1, 2), (2, 1), (2, 3)])
+             sage: G.edges(data=True)
+-            [(1, 2, {'weight': 7}),
+-             (2, 1, {7: {}, 8: {}}),
+-             (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})]
++            OutMultiEdgeDataView([(1, 2, {'weight': 7}), (2, 1, {8: {}, 7: {}}), (2, 3, {4: {}, 5: {}, 6: {}, 7: {}})])
+ 
+         """
+         import networkx
+@@ -1154,7 +1152,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+         import networkx
+         try:
+             if self._nxg.is_multigraph():
+-                for k,d in self._nxg.edge[u][v].iteritems():
++                for u0,v0,k,d in self._nxg.edges([u,v],True,keys=True):
+                     if d.get('weight',None) == l:
+                         self._nxg.remove_edge(u,v,k)
+                         break
+@@ -1223,7 +1221,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+         """
+         cdef dict E
+         try:
+-            E = self._nxg.edge[u][v]
++            E = self._nxg.edges[u,v,0]
+         except KeyError:
+             from networkx import NetworkXError
+             raise NetworkXError("Edge (%s,%s) requested via get_edge_label does not exist."%(u,v))
+@@ -1412,7 +1410,7 @@ class NetworkXGraphBackend(GenericGraphBackend):
+             sage: G.iterator_nbrs(0)
+             <dictionary-keyiterator object at ...>
+         """
+-        return self._nxg.neighbors_iter(v)
++        return self._nxg.neighbors(v)
+ 
+     def iterator_in_nbrs(self, v):
+         """
+diff --git a/src/sage/graphs/digraph.py b/src/sage/graphs/digraph.py
+index 003a8d6bcb..986137a9b0 100644
+--- a/src/sage/graphs/digraph.py
++++ b/src/sage/graphs/digraph.py
+@@ -755,7 +755,7 @@ class DiGraph(GenericGraph):
+             self.allow_multiple_edges(multiedges,check=False)
+             self.allow_loops(loops,check=False)
+             self.add_vertices(data.nodes())
+-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
++            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
+         elif format == 'igraph':
+             if not data.is_directed():
+                 raise ValueError("A *directed* igraph graph was expected. To "+
+@@ -2846,7 +2846,7 @@ class DiGraph(GenericGraph):
+         Using the NetworkX implementation ::
+ 
+             sage: D.topological_sort(implementation = "NetworkX")
+-            [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10]
++            [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
+ 
+         Using the NetworkX recursive implementation ::
+ 
+@@ -2872,9 +2872,7 @@ class DiGraph(GenericGraph):
+               sage: D = DiGraph({ 0:[1,2,3], 4:[2,5], 1:[8], 2:[7], 3:[7],
+               ....:   5:[6,7], 7:[8], 6:[9], 8:[10], 9:[10] })
+               sage: N = D.networkx_graph()
+-              sage: networkx.topological_sort(N)
+-              [4, 5, 6, 9, 0, 1, 2, 3, 7, 8, 10]
+-              sage: networkx.topological_sort_recursive(N)
++              sage: list(networkx.topological_sort(N))
+               [4, 5, 6, 9, 0, 3, 2, 7, 1, 8, 10]
+ 
+         TESTS:
+@@ -2897,10 +2895,7 @@ class DiGraph(GenericGraph):
+ 
+         elif implementation == "NetworkX" or implementation == "recursive":
+             import networkx
+-            if implementation == "NetworkX":
+-                S = networkx.topological_sort(self.networkx_graph(copy=False))
+-            else:
+-                S = networkx.topological_sort_recursive(self.networkx_graph(copy=False))
++            S = list(networkx.topological_sort(self.networkx_graph(copy=False)))
+             if S is None:
+                 raise TypeError('Digraph is not acyclic; there is no topological sort.')
+             else:
+diff --git a/src/sage/graphs/generators/families.py b/src/sage/graphs/generators/families.py
+index 8f81333685..1540ec0dcc 100644
+--- a/src/sage/graphs/generators/families.py
++++ b/src/sage/graphs/generators/families.py
+@@ -197,7 +197,7 @@ def BalancedTree(r, h):
+     gracefully::
+ 
+         sage: graphs.BalancedTree(1, 10)
+-        Balanced tree: Graph on 2 vertices
++        Balanced tree: Graph on 11 vertices
+ 
+         sage: graphs.BalancedTree(-1, 10)
+         Balanced tree: Graph on 1 vertex
+@@ -208,9 +208,6 @@ def BalancedTree(r, h):
+         sage: graphs.BalancedTree(3, 0)
+         Balanced tree: Graph on 1 vertex
+ 
+-        sage: graphs.BalancedTree(5, -2)
+-        Balanced tree: Graph on 0 vertices
+-
+         sage: graphs.BalancedTree(-2,-2)
+         Balanced tree: Graph on 0 vertices
+     """
+diff --git a/src/sage/graphs/graph.py b/src/sage/graphs/graph.py
+index 3550f990ef..490813e619 100644
+--- a/src/sage/graphs/graph.py
++++ b/src/sage/graphs/graph.py
+@@ -1199,7 +1199,7 @@ class Graph(GenericGraph):
+             self.allow_loops(loops, check=False)
+             self.allow_multiple_edges(multiedges, check=False)
+             self.add_vertices(data.nodes())
+-            self.add_edges((u,v,r(l)) for u,v,l in data.edges_iter(data=True))
++            self.add_edges((u,v,r(l)) for u,v,l in data.edges(data=True))
+         elif format == 'igraph':
+             if data.is_directed():
+                 raise ValueError("An *undirected* igraph graph was expected. "+
+@@ -4621,7 +4621,7 @@ class Graph(GenericGraph):
+ 
+             sage: g = Graph([(0,1,0), (1,2,999), (2,3,-5)])
+             sage: g.matching(use_edge_labels=True)
+-            [(1, 2, 999)]
++            [(0, 1, 0), (2, 3, -5)]
+             sage: g.matching(algorithm="LP", use_edge_labels=True)
+             [(1, 2, 999)]
+ 
+@@ -4671,7 +4671,7 @@ class Graph(GenericGraph):
+             else:
+                 for u, v in L:
+                     g.add_edge(u, v)
+-            d = networkx.max_weight_matching(g)
++            d = dict(networkx.max_weight_matching(g).union(t[::-1] for t in networkx.max_weight_matching(g)))
+             if value_only:
+                 if use_edge_labels:
+                     return sum(W[u, v] for u, v in six.iteritems(d) if u < v)
+@@ -6305,7 +6305,7 @@ class Graph(GenericGraph):
+         return networkx.number_of_cliques(self.networkx_graph(copy=False), vertices, cliques)
+ 
+     @doc_index("Clique-related methods")
+-    def cliques_get_max_clique_graph(self, name=''):
++    def cliques_get_max_clique_graph(self):
+         """
+         Return the clique graph.
+ 
+@@ -6336,7 +6336,7 @@ class Graph(GenericGraph):
+             sage: (G.cliques_get_max_clique_graph()).show(figsize=[2,2])
+         """
+         import networkx
+-        return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), name=name, create_using=networkx.MultiGraph()))
++        return Graph(networkx.make_max_clique_graph(self.networkx_graph(copy=False), create_using=networkx.MultiGraph()))
+ 
+     @doc_index("Clique-related methods")
+     def cliques_get_clique_bipartite(self, **kwds):
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-python3-notebook.patch (from rev 319428, sagemath/trunk/sagemath-python3-notebook.patch)
===================================================================
--- sagemath-python3-notebook.patch	                        (rev 0)
+++ sagemath-python3-notebook.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,27 @@
+diff --git a/src/bin/sage-notebook b/src/bin/sage-notebook
+index 74192da240..0ede281aad 100755
+--- a/src/bin/sage-notebook
++++ b/src/bin/sage-notebook
+@@ -96,8 +96,7 @@ class NotebookJupyter(object):
+         if not have_prerequisites():
+             print(self.PREREQUISITE_ERROR)
+             raise SystemExit(1)
+-        from notebook.notebookapp import main
+-        main(argv)
++        os.execvp('jupyter-notebook', ['jupyter-notebook'] + argv)
+ 
+ 
+ class NotebookJupyterlab(object):
+diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py
+index 3912b8cdf5..bd40cdadda 100644
+--- a/src/sage/repl/ipython_kernel/install.py
++++ b/src/sage/repl/ipython_kernel/install.py
+@@ -280,7 +280,6 @@ def have_prerequisites(debug=True):
+         True
+     """
+     try:
+-        from notebook.notebookapp import NotebookApp
+         return True
+     except ImportError:
+         if debug:
+

Copied: sagemath/repos/community-testing-x86_64/sagemath-scipy-1.0.patch (from rev 319428, sagemath/trunk/sagemath-scipy-1.0.patch)
===================================================================
--- sagemath-scipy-1.0.patch	                        (rev 0)
+++ sagemath-scipy-1.0.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,16 @@
+diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
+index 17b5ebb84b..7ce9055cba 100644
+--- a/src/sage/numerical/optimize.py
++++ b/src/sage/numerical/optimize.py
+@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
+                 else:
+                     min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0]
+         elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression):
+-            min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
++            min = optimize.fmin_cobyla(f, x0, cons, **args)
+     elif isinstance(cons, function_type) or isinstance(cons, Expression):
+-        min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
++        min = optimize.fmin_cobyla(f, x0, cons, **args)
+     return vector(RDF, min)
+ 
+ 

Copied: sagemath/repos/community-testing-x86_64/sagemath-singular-4.1.1.patch (from rev 319428, sagemath/trunk/sagemath-singular-4.1.1.patch)
===================================================================
--- sagemath-singular-4.1.1.patch	                        (rev 0)
+++ sagemath-singular-4.1.1.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,94 @@
+diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd
+index 676544ab1e..5c8639d362 100644
+--- a/src/sage/libs/singular/decl.pxd
++++ b/src/sage/libs/singular/decl.pxd
+@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h":
+ 
+     int n_NumberOfParameters(const n_Procs_s* r)
+ 
+-    ctypedef struct poly "polyrec":
++    ctypedef struct poly "spolyrec":
+         poly *next
+         number *coef
+         unsigned long exp[1]
+@@ -632,7 +632,7 @@ cdef extern from "singular/Singular/libsingular.h":
+ 
+     # divide monomial p by monomial q, p,q const
+ 
+-    poly *pDivide(poly *p,poly *q)
++    poly *pMDivide(poly *p,poly *q)
+ 
+     # return the i-th power of p; p destroyed, requires global ring
+ 
+diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
+index 089524d6b4..ce6d58fc6f 100644
+--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
+@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport (
+     n_IsUnit, n_Invers,
+     p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q,
+     p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup,
+-    omFree, pDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy,
+-    pDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy,
++    omFree, pMDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy,
++    pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy,
+     p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete,
+     p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize,
+     idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD,
+@@ -1692,8 +1697,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
+         if not g._poly:
+             raise ZeroDivisionError
+ 
+-        if r!=currRing: rChangeCurrRing(r)  # pDivide
+-        res = pDivide(f._poly, g._poly)
++        if r!=currRing: rChangeCurrRing(r)  # pMDivide
++        res = pMDivide(f._poly, g._poly)
+         if coeff:
+             if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
+                 n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
+@@ -1852,8 +1857,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_generic):
+                    and (<MPolynomial_libsingular>g) \
+                    and g.parent() is self \
+                    and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r):
+-                if r!=currRing: rChangeCurrRing(r)  # pDivide
+-                flt = pDivide(f._poly, (<MPolynomial_libsingular>g)._poly)
++                if r!=currRing: rChangeCurrRing(r)  # pMDivide
++                flt = pMDivide(f._poly, (<MPolynomial_libsingular>g)._poly)
+                 #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r)
+                 p_SetCoeff(flt, n_Init(1, r), r)
+                 return new_MP(self,flt), g
+@@ -4049,10 +4054,10 @@ cdef class MPolynomial_libsingular(MPolynomial):
+             if _right.is_monomial():
+                 p = _self._poly
+                 quo = p_ISet(0,r)
+-                if r != currRing: rChangeCurrRing(r)   # pDivide
++                if r != currRing: rChangeCurrRing(r)   # pMDivide
+                 while p:
+                     if p_DivisibleBy(_right._poly, p, r):
+-                        temp = pDivide(p, _right._poly)
++                        temp = pMDivide(p, _right._poly)
+                         p_SetCoeff0(temp, n_Copy(p_GetCoeff(p, r), r), r)
+                         quo = p_Add_q(quo, temp, r)
+                     p = pNext(p)
+diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx
+index 3b45a38419..c0227fd364 100644
+--- a/src/sage/rings/polynomial/plural.pyx
++++ b/src/sage/rings/polynomial/plural.pyx
+@@ -999,7 +999,7 @@ cdef class NCPolynomialRing_plural(Ring):
+         if not g._poly:
+             raise ZeroDivisionError
+ 
+-        res = pDivide(f._poly,g._poly)
++        res = pMDivide(f._poly,g._poly)
+         if coeff:
+             if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
+                 n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
+@@ -1194,7 +1194,7 @@ cdef class NCPolynomialRing_plural(Ring):
+             if isinstance(g, NCPolynomial_plural) \
+                    and (<NCPolynomial_plural>g) \
+                    and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r):
+-                flt = pDivide(f._poly, (<NCPolynomial_plural>g)._poly)
++                flt = pMDivide(f._poly, (<NCPolynomial_plural>g)._poly)
+                 #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<NCPolynomial_plural>g)._poly, r), r), r)
+                 p_SetCoeff(flt, n_Init(1, r), r)
+                 return new_NCP(self,flt), g

Copied: sagemath/repos/community-testing-x86_64/sagemath-threejs.patch (from rev 319428, sagemath/trunk/sagemath-threejs.patch)
===================================================================
--- sagemath-threejs.patch	                        (rev 0)
+++ sagemath-threejs.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,11 @@
+--- a/src/sage/repl/rich_output/display_manager.py
++++ b/src/sage/repl/rich_output/display_manager.py
+@@ -744,7 +744,7 @@ class DisplayManager(SageObject):
+         """
+         if online:
+             from sage.misc.package import installed_packages
+-            version = installed_packages()['threejs']
++            version = 'r90'
+             return """
+ <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/build/three.min.js"></script>
+ <script src="https://cdn.rawgit.com/mrdoob/three.js/{0}/examples/js/controls/OrbitControls.js"></script>

Copied: sagemath/repos/community-testing-x86_64/test-optional.patch (from rev 319428, sagemath/trunk/test-optional.patch)
===================================================================
--- test-optional.patch	                        (rev 0)
+++ test-optional.patch	2018-05-07 21:08:27 UTC (rev 319429)
@@ -0,0 +1,27 @@
+--- src/sage/doctest/control.py.orig       2016-10-20 19:39:53.714618246 +0200
++++ src/sage/doctest/control.py    2016-10-20 19:40:15.158049920 +0200
+@@ -326,24 +326,6 @@
+             if "all" in options.optional:
+                 # Special case to run all optional tests
+                 options.optional = True
+-            else:
+-                # We replace the 'optional' tag by all optional
+-                # packages for which the installed version matches the
+-                # latest available version (this implies in particular
+-                # that the package is actually installed).
+-                if 'optional' in options.optional:
+-                    options.optional.discard('optional')
+-                    from sage.misc.package import list_packages
+-                    for pkg in list_packages('optional', local=True).values():
+-                        if pkg['installed_version'] == pkg['remote_version']:
+-                            options.optional.add(pkg['name'])
+-
+-                # Check that all tags are valid
+-                for o in options.optional:
+-                    if not optionaltag_regex.search(o):
+-                        raise ValueError('invalid optional tag {!r}'.format(o))
+-
+-                options.optional |= auto_optional_tags
+
+         self.options = options
+         self.files = args



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