Sage 6.4.beta3 released
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Volker Braun
Sep 11, 2014, 8:30:28 AM9/11/14
to sage-r...@googlegroups.com
The "develop" git branch has been updated. Alternatively, download http://boxen.math.washington.edu/home/release/sage-6.4.beta3.tar.gz
Mini-changelog:
c1cc800 Trac #16912: Upgrade Cython to 0.21
01ab218 Trac #16945: Switch buckygen package to sage-git directory layout
8aa4263 Trac #16944: GF(q) -> PARI: always return FFELT
e674fd9 Trac #16228: make tachyon respect standard verbosity settings
05e12f8 Trac #16915: Remove workaround for old Pyrex in element_givaro.pyx
34a1da0 Trac #16950: Update citation HKW2014 to reflect new revision of that article on arxiv.org
c7ba064 Trac #15915: add discrete Gaussian samplers to Sage
7e45fb3 Trac #16827: Use atomic_write in sage-preparse
9b3c95f Trac #16951: Make random_point() for elliptic curves over a finite field uniform
2d02af5 Trac #13627: implement xgcd for padics
d28bb44 Trac #15057: SymPy conversions for symbolic functions that are missing them
f497c57 Trac #16943: FiniteStateMachine._latex_: convert angles to floats where necessary.
01a1bb7 Trac #14637: Maxima should simplify acos(cos(x))
66ff967 Trac #16941: Add a hold parameter for symbolic integrals
7a2e679 Trac #16641: Add qepcad to documentation
4bafb76 Trac #16745: Random OperationalError: disk I/O error
bbb459c Trac #11631: L-series attached to cusp forms are broken
72301ea Trac #16916: cuspform_lseries() method for a new form has precision issues
eedcf03 Trac #16901: cythonized function in combinatorial designs must be interruptible
e01367d Trac #16853: Replace some cmp parameters by key paramters
f43e353 Trac #16238: Correct call convention for isogenies
61429ad Trac #16245: Compose isogenies
13ead6f Trac #16930: Deprecate non-polynomial modulus argument in constructor of implementations of finite fiel
08791ef Trac #16902: Advertise sig_check() better in the developers manual
dbda3f3 Trac #8373: Construct finite fields with primitive defining polynomial
3e181a6 Trac #16851: Implement direct sum and tensor products for chain complexes and Koszul complexes
67181f0 Trac #15946: Cython warnings about mpz_t ("... referenced before assignment")
21680c0 Trac #16887: Wider MOLS table plus better interface
7fcdd27 Trac #16884: Quasi-difference matrices (database+is_QDM)
7528eb3 Trac #16879: OA caching in C
6b4c714 Trac #16914: Generic graphs / is_subgraph, documentation typo
6d01129 Trac #16906: Fix trivial docstring indendation error in misc.decorators.decorator_keywords
17d28ee Trac #16903: bugfix for database_cremona_ellcurve optional spkg
7b84cb0 Trac #16881: Rename number field __pari_* attributes to _pari_*
0d06eaf Trac #16838: make affine and projective dehomogenize and homogenize work together
0eb8bfb Trac #16799: clique polynomial of a graph
f447f81 Trac #16043: Hilbert Symbol introduces bugs from Pari
7f51933 Trac #16927: Add Sage interface for PARI functions ffprimroot, fflog, fforder
b6ef3c4 Trac #16913: Error in prev()
11c3bad Trac #16910: Get rid of mpz_t_offset hacks in integer.pyx
f186527 Trac #16894: bug in is_square over number fields
28a8085 Trac #16583: Clean up FLINT declarations
a7a2b10 Trac #16066: Python 3 preparation: Handle removed execfile() function
1eb2427 Trac #16065: Python 3 preparation: Handle removed exec statement
126311d Trac #16023: remove deprecated code in functions/ and symbolic/
ac17396 Trac #16651: Buggy to_poly_solve option
1030f64 Trac #16921: IPython 2.2.0
7cb1dd5 Trac #16858: Print RDF and CDF elements with more digits
a0aa3b6 Trac #16889: Doctest tolerance: allow spaces and use intervals
Ralf Stephan
Sep 11, 2014, 11:04:04 AM9/11/14
to sage-r...@googlegroups.com
sage -t --long src/sage/stats/distributions/discrete_gaussian_integer.pyx
**********************************************************************
File "src/sage/stats/distributions/discrete_gaussian_integer.pyx",
line 262, in sage.stats.distributions.discrete_gaussian_integer.DiscreteGaussianDistributionIntegerSampler.__init__
Failed example:
min(l), max(l), abs(mean(l)-2.5) < 0.01
Expected:
(-2, 7, True)
Got:
(-2, 6, True)
this is after sage -upgrade, make, make doc-clean, make doc, make ptestlong
on opensuse 12.3
Regards,
**********************************************************************
File "src/sage/stats/distributions/discrete_gaussian_integer.pyx",
line 262, in sage.stats.distributions.discrete_gaussian_integer.DiscreteGaussianDistributionIntegerSampler.__init__
Failed example:
min(l), max(l), abs(mean(l)-2.5) < 0.01
Expected:
(-2, 7, True)
Got:
(-2, 6, True)
this is after sage -upgrade, make, make doc-clean, make doc, make ptestlong
on opensuse 12.3
Regards,
Volker Braun
Sep 11, 2014, 11:24:24 AM9/11/14
to sage-r...@googlegroups.com
This happened once before at http://trac.sagemath.org/ticket/15915, apparently the fix was not sufficient. Can you
I've created http://trac.sagemath.org/ticket/16968 for this issue, can you add a description about your machine there?
Samuel Lelièvre
Sep 17, 2014, 1:09:36 PM9/17/14
to sage-release
Volker wrote:
> Sage 6.4.beta3 released
- The build on OS X 10.9 went fine.
- On OS X 10.10 Public Beta 3, with XCode 6.1 Beta and
Apple's command-line tools (which ship Apple's gcc-4.2.1),
the build fails while trying to build gcc-4.7.3 (known bug).
- Adding to that setup homebrew's gcc-4.9.1, the build
fails while trying to build cython-0.21. The logs are at:
http://www.math.u-psud.fr/~lelievre/t/20140917/install.log.tgz
http://www.math.u-psud.fr/~lelievre/t/20140917/config.log.tgz
http://www.math.u-psud.fr/~lelievre/t/20140917/cython-0.21.log.tgz
and below is the full cython-0.21.log.
-----
Found local metadata for cython-0.21
Found local sources at
/Users/s/builds/sage-6.4.beta3/upstream/cython-0.21.tar.gz
Checksum: f5784539870715e33b51374e9c4451ff6ff21c7f vs
f5784539870715e33b51374e9c4451ff6ff21c7f
cython-0.21
====================================================
Setting up build directory for cython-0.21
Finished set up
****************************************************
Host system:
Darwin Samuels-MacBook-Air.local 14.0.0 Darwin Kernel Version 14.0.0:
Mon Sep 8 05:27:41 PDT 2014; root:xnu-2782.1.96~5/RELEASE_X86_64
x86_64
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.1/lto-wrapper
Target: x86_64-apple-darwin14.0.0
Configured with: ../configure --build=x86_64-apple-darwin14.0.0
--prefix=/usr/local/Cellar/gcc/4.9.1
--enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-4.9
--with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr
--with-mpc=/usr/local/opt/libmpc --with-cloog=/usr/local/opt/cloog
--with-isl=/usr/local/opt/isl --with-system-zlib
--enable-version-specific-runtime-libs --enable-libstdcxx-time=yes
--enable-stage1-checking --enable-checking=release --enable-lto
--disable-werror --with-pkgversion='Homebrew gcc 4.9.1'
--with-bugurl=https://github.com/Homebrew/homebrew/issues
--enable-plugin --disable-nls --enable-multilib
Thread model: posix
gcc version 4.9.1 (Homebrew gcc 4.9.1)
****************************************************
Compiling module Cython.Plex.Scanners ...
ERROR: No module named _scproxy
Extension module compilation failed, looks like Cython cannot run
properly on this system. To work around this, pass the option
"--no-cython-compile". This will install a pure Python version of
Cython without compiling its own sources.
Traceback (most recent call last):
File "setup.py", line 266, in <module>
compile_cython_modules(cython_profile, cython_compile_more,
cython_with_refnanny)
File "setup.py", line 210, in compile_cython_modules
result = compile(pyx_source_file)
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Main.py",
line 622, in compile
return compile_single(source, options, full_module_name)
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Main.py",
line 575, in compile_single
return run_pipeline(source, options, full_module_name)
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Main.py",
line 400, in run_pipeline
from . import Pipeline
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Pipeline.py",
line 9, in <module>
from .Visitor import CythonTransform
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Visitor.py",
line 14, in <module>
from . import ExprNodes
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/ExprNodes.py",
line 38, in <module>
from .Annotate import AnnotationItem
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Annotate.py",
line 9, in <module>
from xml.sax.saxutils import escape as html_escape
File "/Users/s/builds/sage-6.4.beta3/local/lib/python/xml/sax/saxutils.py",
line 6, in <module>
import os, urlparse, urllib, types
File "/Users/s/builds/sage-6.4.beta3/local/lib/python/urllib.py",
line 1399, in <module>
from _scproxy import _get_proxy_settings, _get_proxies
ImportError: No module named _scproxy
Error installing Cython
real 0m0.325s
user 0m0.279s
sys 0m0.042s
************************************************************************
Error installing package cython-0.21
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/Users/s/builds/sage-6.4.beta3/logs/pkgs/cython-0.21.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21
and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21'
&& '/Users/s/builds/sage-6.4.beta3/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
> Sage 6.4.beta3 released
> The "develop" git branch has been updated. Alternatively, download http://boxen.math.washington.edu/home/release/sage-6.4.beta3.tar.gz
Thank you for this new release!
- The build on OS X 10.9 went fine.
- On OS X 10.10 Public Beta 3, with XCode 6.1 Beta and
Apple's command-line tools (which ship Apple's gcc-4.2.1),
the build fails while trying to build gcc-4.7.3 (known bug).
- Adding to that setup homebrew's gcc-4.9.1, the build
fails while trying to build cython-0.21. The logs are at:
http://www.math.u-psud.fr/~lelievre/t/20140917/install.log.tgz
http://www.math.u-psud.fr/~lelievre/t/20140917/config.log.tgz
http://www.math.u-psud.fr/~lelievre/t/20140917/cython-0.21.log.tgz
and below is the full cython-0.21.log.
-----
Found local metadata for cython-0.21
Found local sources at
/Users/s/builds/sage-6.4.beta3/upstream/cython-0.21.tar.gz
Checksum: f5784539870715e33b51374e9c4451ff6ff21c7f vs
f5784539870715e33b51374e9c4451ff6ff21c7f
cython-0.21
====================================================
Setting up build directory for cython-0.21
Finished set up
****************************************************
Host system:
Darwin Samuels-MacBook-Air.local 14.0.0 Darwin Kernel Version 14.0.0:
Mon Sep 8 05:27:41 PDT 2014; root:xnu-2782.1.96~5/RELEASE_X86_64
x86_64
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/4.9.1/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.1/lto-wrapper
Target: x86_64-apple-darwin14.0.0
Configured with: ../configure --build=x86_64-apple-darwin14.0.0
--prefix=/usr/local/Cellar/gcc/4.9.1
--enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-4.9
--with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr
--with-mpc=/usr/local/opt/libmpc --with-cloog=/usr/local/opt/cloog
--with-isl=/usr/local/opt/isl --with-system-zlib
--enable-version-specific-runtime-libs --enable-libstdcxx-time=yes
--enable-stage1-checking --enable-checking=release --enable-lto
--disable-werror --with-pkgversion='Homebrew gcc 4.9.1'
--with-bugurl=https://github.com/Homebrew/homebrew/issues
--enable-plugin --disable-nls --enable-multilib
Thread model: posix
gcc version 4.9.1 (Homebrew gcc 4.9.1)
****************************************************
Compiling module Cython.Plex.Scanners ...
ERROR: No module named _scproxy
Extension module compilation failed, looks like Cython cannot run
properly on this system. To work around this, pass the option
"--no-cython-compile". This will install a pure Python version of
Cython without compiling its own sources.
Traceback (most recent call last):
File "setup.py", line 266, in <module>
compile_cython_modules(cython_profile, cython_compile_more,
cython_with_refnanny)
File "setup.py", line 210, in compile_cython_modules
result = compile(pyx_source_file)
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Main.py",
line 622, in compile
return compile_single(source, options, full_module_name)
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Main.py",
line 575, in compile_single
return run_pipeline(source, options, full_module_name)
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Main.py",
line 400, in run_pipeline
from . import Pipeline
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Pipeline.py",
line 9, in <module>
from .Visitor import CythonTransform
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Visitor.py",
line 14, in <module>
from . import ExprNodes
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/ExprNodes.py",
line 38, in <module>
from .Annotate import AnnotationItem
File "/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21/src/Cython/Compiler/Annotate.py",
line 9, in <module>
from xml.sax.saxutils import escape as html_escape
File "/Users/s/builds/sage-6.4.beta3/local/lib/python/xml/sax/saxutils.py",
line 6, in <module>
import os, urlparse, urllib, types
File "/Users/s/builds/sage-6.4.beta3/local/lib/python/urllib.py",
line 1399, in <module>
from _scproxy import _get_proxy_settings, _get_proxies
ImportError: No module named _scproxy
Error installing Cython
real 0m0.325s
user 0m0.279s
sys 0m0.042s
************************************************************************
Error installing package cython-0.21
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/Users/s/builds/sage-6.4.beta3/logs/pkgs/cython-0.21.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21
and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/cython-0.21'
&& '/Users/s/builds/sage-6.4.beta3/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Volker Braun
Sep 17, 2014, 3:35:04 PM9/17/14
to sage-r...@googlegroups.com
In your python build log should be more about why it didn't build the _scproxy.so module....
Samuel Lelièvre
Sep 18, 2014, 10:00:41 AM9/18/14
to sage-release
The python build log is here:
http://www.math.u-psud.fr/~lelievre/t/20140917/python-2.7.8.log.tgz
It has a number of warnings.
Here is the excerpt about _scproxy:
building '_scproxy' extension
creating build/temp.macosx-10.10-x86_64-2.7/Mac
creating build/temp.macosx-10.10-x86_64-2.7/Mac/Modules
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-I/Users/s/builds/sage-6.4.beta3/local/include -I. -IInclude
-I./Include -I/usr/local/include
-I/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/python-2.7.8/src/Include
-I/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/python-2.7.8/src
-c ./Mac/Modules/_scproxy.c -o
build/temp.macosx-10.10-x86_64-2.7/./Mac/Modules/_scproxy.o
In file included from /usr/include/dispatch/dispatch.h:51:0,
from
/System/Library/Frameworks/CoreFoundation.framework/Headers/CFStream.h:15,
from
/System/Library/Frameworks/CoreFoundation.framework/Headers/CFPropertyList.h:13,
from
/System/Library/Frameworks/CoreFoundation.framework/Headers/CoreFoundation.h:55,
from
/System/Library/Frameworks/SystemConfiguration.framework/Headers/SystemConfiguration.h:29,
from ./Mac/Modules/_scproxy.c:6:
/usr/include/dispatch/object.h:143:15: error: expected identifier or
'(' before '^' token
typedef void (^dispatch_block_t)(void);
^
/usr/include/dispatch/object.h:362:3: error: unknown type name
'dispatch_block_t'
dispatch_block_t notification_block);
^
./Mac/Modules/_scproxy.c: In function 'get_proxy_settings':
./Mac/Modules/_scproxy.c:67:50: warning: the comparison will always
evaluate as 'true' for the address of
'kSCPropNetProxiesExcludeSimpleHostnames' will never be NULL
[-Waddress]
if (&kSCPropNetProxiesExcludeSimpleHostnames != NULL) {
^
> --
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http://www.math.u-psud.fr/~lelievre/t/20140917/python-2.7.8.log.tgz
It has a number of warnings.
Here is the excerpt about _scproxy:
building '_scproxy' extension
creating build/temp.macosx-10.10-x86_64-2.7/Mac
creating build/temp.macosx-10.10-x86_64-2.7/Mac/Modules
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-I/Users/s/builds/sage-6.4.beta3/local/include -I. -IInclude
-I./Include -I/usr/local/include
-I/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/python-2.7.8/src/Include
-I/Users/s/builds/sage-6.4.beta3/local/var/tmp/sage/build/python-2.7.8/src
-c ./Mac/Modules/_scproxy.c -o
build/temp.macosx-10.10-x86_64-2.7/./Mac/Modules/_scproxy.o
In file included from /usr/include/dispatch/dispatch.h:51:0,
from
/System/Library/Frameworks/CoreFoundation.framework/Headers/CFStream.h:15,
from
/System/Library/Frameworks/CoreFoundation.framework/Headers/CFPropertyList.h:13,
from
/System/Library/Frameworks/CoreFoundation.framework/Headers/CoreFoundation.h:55,
from
/System/Library/Frameworks/SystemConfiguration.framework/Headers/SystemConfiguration.h:29,
from ./Mac/Modules/_scproxy.c:6:
/usr/include/dispatch/object.h:143:15: error: expected identifier or
'(' before '^' token
typedef void (^dispatch_block_t)(void);
^
/usr/include/dispatch/object.h:362:3: error: unknown type name
'dispatch_block_t'
dispatch_block_t notification_block);
^
./Mac/Modules/_scproxy.c: In function 'get_proxy_settings':
./Mac/Modules/_scproxy.c:67:50: warning: the comparison will always
evaluate as 'true' for the address of
'kSCPropNetProxiesExcludeSimpleHostnames' will never be NULL
[-Waddress]
if (&kSCPropNetProxiesExcludeSimpleHostnames != NULL) {
^
> 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
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> To post to this group, send email to sage-r...@googlegroups.com.
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> For more options, visit https://groups.google.com/d/optout.
Volker Braun
Sep 18, 2014, 10:14:56 AM9/18/14
to sage-r...@googlegroups.com
On Thursday, September 18, 2014 3:00:41 PM UTC+1, Samuel Lelievre wrote:
typedef void (^dispatch_block_t)(void);
^
/usr/include/dispatch/object.h:362:3: error: unknown type name
That header is Objective-C, which should never have been included when compiling C sources. Most likely an OSX bug. You can send them a bug report if you like talking at walls...
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