SAGE-2.8.15!
William Stein
Sage 2.8.15 has been released. It is available at
http://sagemath.org/download.html
The following people contributed this release:
- Craig Citro
- Dan Drake
- David Harvey
- Michael Abshoff
- Martin Albreecht
- Jen Balakrishnan
- Robert Bradshaw
- Jason Grout
- Mike Hansen
- Leif Hille
- Josh Kantor
- Robert Miller
- Joel Mohler
- David Roe
- Jaap Spies
- William Stein
- Brian "trixb4kidz"
- Carl Witty
- Paul Zimmermann
Cheers,
Michael Abshoff (release chair), William Stein
* Major Features, New Spkgs and Bugfixes
Singular was updated to the latest 3-0-4 release. But neither PolyBoRi
nor ATLAS made it into the final release. But the vast majority of the
prep work needed to make ATLAS a standard spkg was finally done in
this release cycle. PolyBoRi will probably become an optional spkg
first until all the details have been worked out.
We closed a total of 62 tickets, for details see
http://www.sagetrac.org/sage_trac/query?status=closed&milestone=sage-2.8.15
for details.
Closed Tickets:
rc1 - merged:
#1074: Martin Albrecht: Singular segfault with monitor("","io"); -
fixed upstream by Hans Scher L-series
#1309: Robert Miller: graphs: generate trees
#1356: Carl Witty: fix bug when taking abs() of exactly known QQbar
#1357: Carl Witty: the polynomial .roots() method should work with
ring=QQbar
#1368: William Stein: algorithm for computing quotient was sometimes
wrong
#1372: Michael Abshoff: dokchitser.py doctest failure (numerical
noise)
#1973: William Stein, Carl Witty: improve doctests of
quotient_module.py
#1374: Carl Witty, William Stein: segfault in coercion with matrices
and ints
#1375: William Stein: tutorial texing typo issue
#1376: Carl Witty, Michael Abshoff: fix numerical doctest failures in
2.8.15.rc0
alpha2 - Merged:
#787: William Stein: quotient spaces of vector spaces
#799: Leif Hille, William Stein: fix tachyon bug
#962: Mike Hansen: automatic precision extension for long decimal
literals does very strange things
#1128: David Roe, Robert Bradshaw: Coercion of complex numbers
#1160: William Stein: *major* bug in using the sage notebook as a
maxima notebook
#1179: Robert Miller: change all #!/bin/sh to #!/bin/bash in
$SAGE_LOCAL/bin (Solaris related)
#1184: Michael Abshoff: OSX 10.4: moving sage breaks recompile -> NTL
related
#1201: William Stein: add gramm-schmidt to sage
#1208: Jaap Spies: Faster _choose in matrix2.py
#1211: David Harvey: NTL crash in polynomial remainder over ZZ
#1222: Josh Kantor: cvxopt import trouble on PPC OSX 10.4
#1269: Carl Witty: make sage -t --omega work
#1275: Carl Witty: implementation of QQbar
#1290: Dan Drake, William Stein: add computation of Rencontres numbers
#1292: Carl Witty: fix bug in polynomial root finding mod n
#1298: Josh Kantor: build lapack on OSX for the ATLAS build
#1327: Josh Kantor: Solaris: scipy import error - fortran compiler
related
#1342: William Stein: very serious bug in number field residue_field
#1349: to avoid massive confusion, make the default notebook location
$HOME/.sage/notebook
#1353: Robert Miller: fix easy bug in graph_database.py
#1354: Michael Abshoff: Solaris modp 64 bit fix
#1355: Michael Abshoff: numerical noise doctest failures in
rings/polynomial/[complex_roots.py|polynomial_element.pyx]
#1361: Robert Miller: reimplement graph generation
#1364: William Stein: sage/modules/quotient_module.py doctest failure
alpha1 - Merged:
#644: Mike Hansen: fix "(sin + cos)(1) does not work"
#1148: David Harvey, Robert Bradshaw: valuation doesn't work for
rational numbers
#1214: Mike Hansen: error in polynomial ideal membership testing
#1249: Robert Miller: fixes bug in graph plotting with partitions
#1265: Paul Zimmermann: documentation typos
#1279: Martin Abrecht: LLL on "tall" matrices immediately crashes sage
#1280: Mike Hansen: make Permutation(range(10)).random() fast instead
of dog slow.
#1333: William Stein: fix a major inefficiency in floating point
square root computation in Sage
#1334: David Harvey: Constant polynomial can't be converted to
rational
#1341: Josh Kantor: add script so that which_fortran returns g95 or
gfortran
#1350: Mike Hansen: sage-2.8.15.alpha0 doctest error in plot.py
#1352: Mike Hansen: doctest error in 2.8.15.alpha0
polynomial_element.pyx
alpha0 - Merged:
#645: Mike Hansen: multi-argument call for symbolic expressions
#847: Mike Hansen: rewrite the symbolic calculus package to do
evaluation/simplification without recursion
#1107: William Stein: add minkowski bound function for number fields
#1111: Mike Hansen: Symbolic equation expand left and right
#1134: David Harvey: optimize creating elements of orders and number
fields by coercing in lists [I left this ticket open fow now
- see comment]
#1141: Joel Mohler: improve Number Field elements arithmetic speed
#1268: Carl Witty: new version of MPFI.spkg
#1270: Carl Witty: implement complex intervals
#1273: Carl Witty: implement complex root isolation
#1275: Carl Witty: implementation of QQbar
#1295: Jason Grout: Added code to create the butterfly graph
#1330: Michael Abshoff: Solaris: fix sympy doctest numerical noise
#1331: Michael Abshoff: Solaris: fix complex_double doctest numerical
noise
#1335: Michael Abshoff: Linux PPC: lcalc doctest failure
#1336: Michael Abshoff: Linux PPC:
rings/polynomial/polynomial_element.pyx doctest failure
#1345: Mike Hansen: I is sometimes wrapped in SymbolicConstant,
sometimes not
Reviewers: Carl Witty, William Stein, Mike Hansen, Robert Miller,
Michael Abshoff; apologies to anybody I forgot.
Feeback: Jaap Spies, Justin Walker, apologies to anybody I forgot.
* Known Issues with 2.8.15
- FLINT might misbuild due to missing Python
* Upcoming Releases
Sage 2.9 is planned for the end of this week. Proposed major features
are:
- R
- ATLAS BLAS/Lapack
- FLINT 1.0
* Coverage
For 2.8.15:
Overall weighted coverage score: 34.8%
Total number of functions: 17743
Compared to 2.8.13 this is an increase by 0.4%.
* About Sage (http://www.sagemath.org)
Sage is developed by volunteers and combines 71 open source packages.
It is available for download from sagemath.org and its mirrors in
source or binary form. If you have any questions and/or problems
please report them to the google groups sage-devel, sage-support,
sage-forum or sage-newbie. You can also drop by in #sage-devel in
freenode.
--
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org
Andrzej Giniewicz
that's great news... I'm just upgrading it to look around asap... :)
btw, is it really true that R interface is so-almost-ready that it
could be included in release planned for end of week so in few days? I
would be quite amazed to see it so soon :)
regards,
Andrzej Giniewicz.
mabshoff
On Dec 4, 11:24 am, Andrzej Giniewicz <ggi...@gmail.com> wrote:
> WooHoo :)
>
> that's great news... I'm just upgrading it to look around asap... :)
>
> btw, is it really true that R interface is so-almost-ready that it
> could be included in release planned for end of week so in few days? I
> would be quite amazed to see it so soon :)
little integration work into Python needs to be done. It will probably
take a while to expose all the functionality desired by Sage
developers directly, but we need to start by including it.
> regards,
> Andrzej Giniewicz.
Cheers,
Michael
gginiu
> There already is an optional/experimental R.spkg and because of rpy
> little integration work into Python needs to be done. It will probably
> take a while to expose all the functionality desired by Sage
> developers directly, but we need to start by including it.
well, then if there is anything I can help with - from testing to
whatever - you can count me in :) I'm already downloading it :)
A.
mabshoff
taking point on this, but William also certainly wants R to happen. It
might be a good idea to meet in IRC at some point this week and do an
integration/testing session with interested people.
> A.
Cheers,
Michael
William Stein
Please type
sage: install_package('sage -i r-2.6.1rc.p1')
and report back whether the install works for you or not (it's an experimental
package still, which means that it's likely to *not* work for a lot of people).
If it does install, try this:
sage: import rpy
sage: rpy.r.t_test(range(100))
Check out
rpy.sourceforge.net
for more discussion about rpy, which provides a very
fast interface to essentially all the functionality of R.
NOTE: As of now, you'll probably want to do
sage: RealNumber = float; Integer = int
to turn off preparsing of floats and ints when using R, since
the patch for making R play nicely with Sage types isn't in
yet.
William
gginiu
> sage: install_package('sage -i r-2.6.1rc.p1')
I actually installed through command line, but it's mostly same - it
went ok, but.....
> and report back whether the install works for you or not (it's an experimental
> package still, which means that it's likely to *not* work for a lot of people).
I had to edit manually in 2 places, first $SAGE_HOME/local/bin/R has
variable R_HOME_DIR pointing to build dir instead of install dir,
after changing it to right dir I was able to import rpy, because
before it failed...
> If it does install, try this:
>
> sage: import rpy
I did:
sage: from rpy import *
and it worked so quite ok... but not exactly yet :)... at first when I
wanted to check r object I was getting traceback about missing
variable, after change in file rpy.py in line 312 from
Rver = self.__getitem__('R_version_string')
to
Rver = self.__getitem__('R.version.string')
it started to report version, it said:
RPy version 1.0-RC3 [R version 2.6.1 RC (2007-11-24 r43532)]
so ok...
> sage: rpy.r.t_test(range(100))
that test works like a charm...
> Check out
> rpy.sourceforge.net
> for more discussion about rpy, which provides a very
> fast interface to essentially all the functionality of R.
> NOTE: As of now, you'll probably want to do
> sage: RealNumber = float; Integer = int
> to turn off preparsing of floats and ints when using R, since
> the patch for making R play nicely with Sage types isn't in
> yet.
I noticed Integer -> int problem when I was trying
http://rpy.sourceforge.net/rpy_demo.html, got without glitch to some
place, now I try to get:
sage: r.png('faithful_histogram.png',width=int(733),height=int(550))
but no luck currently, anyway I'm still looking around... :)
regards,
Andrzej.
PS.: maybe this should be in separate topic or other list? currently I
use only "reply" from browser, but I think there will be lot more
reports about this :)
William Stein
>
> Hi,
>
> > sage: install_package('sage -i r-2.6.1rc.p1')
>
> I actually installed through command line, but it's mostly same - it
> went ok, but.....
>
> > and report back whether the install works for you or not (it's an experimental
> > package still, which means that it's likely to *not* work for a lot of people).
>
> I had to edit manually in 2 places, first $SAGE_HOME/local/bin/R has
> variable R_HOME_DIR pointing to build dir instead of install dir,
> after changing it to right dir I was able to import rpy, because
> before it failed...
Actually, I had posted the wrong direction -- it's still the case that R builds
in the build directory, the install points to that ("make install" for R
doesn't work like for a normal program), then the build directory gets deleted.
See this thread on R in SAge, which has better directions:
In particular, it is best to build like this
sage -f -m r-2.6.1rc.p1
to leave the build directory around afterwards.
I was able to get the image to work last time I tried, so it's definitely
possible.
-- Wiliam
Andrzej Giniewicz
> possible.
<class 'rpy.RException'>: Error in function (filename = "Rplot
%03d.png", width = 480, height = 480, :
X11 is not available
and well...... that's both from console and notebook, and from plain
R /opt/sage/local/bin/R... just like if it was compiled without
graphics support, probably it could work if --with-x11 or so... and it
seem it's the case because of hack from spkg-install:
# I have problems with this on OSX Intel 10.5.1 -- for now just turn
it off.
# It will be good to get something fully working before worrying about
X.
#if [ -f /usr/include/X11/Xwindows.h ]; then
# XSUPPORT=yes
#else
XSUPPORT=no
#fi
so from it I guess images are left for later :) as I'm on Linux I will
uncomment this to test them.
regards,
Andrzej.
William Stein
(1) I very much thought that I had done graphics with the above
build options using png. Without those options R will definitely fail
to build on many test platforms, by the way.
(2) I don't see why X11 should be necessary to generate png files
using R -- the whole point of png's should be to avoid having to
use X11.
That said, I could be wrong about some of the above. Does R really
require X11 as a dependency just to do png graphics? That would suck.
William
William Stein
(1) I very much thought that I had done graphics with the above
build options using png. Without those options R will definitely fail
to build on many test platforms, by the way.
(2) I don't see why X11 should be necessary to generate png files
using R -- the whole point of png's should be to avoid having to
use X11.
That said, I could be wrong about some of the above. Does R really
require X11 as a dependency just to do png graphics? That would suck.
OK -- I just retested this on my *linux* install, and indeed, creating
png's doesn't work because of no X11. How annoying.
William
Andrzej Giniewicz
version from that package outside of sage, I get that error about
X11...
gginiu
http://tolstoy.newcastle.edu.au/R/e2/help/06/10/3553.html - seem there
is optional package that can deal with it
Justin C. Walker
On Dec 3, 2007, at 23:27 , William Stein wrote:
>
> Hello folks,
>
> Sage 2.8.15 has been released. It is available at
>
> http://sagemath.org/download.html
Built and tested w/o errors on Mac OS X, as follows, both with
"parallel make":
10.4.11 (Dual Quad-Core Xeon -j6):
real 63m1.611s
user 48m35.838s
sys 25m26.978s
All tests passed!
Total time for all tests: 2366.0 seconds
10.5.1 (Core Duo, -j2):
real 89m5.315s
user 74m17.804s
sys 16m57.508s
All tests passed!
Total time for all tests: 2552.2 seconds
Still seeing mwrank crashing during the tests (10.5), but no comment
in the logs.
Justin
--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
My wife 'n kids 'n dogs are gone,
I can't get Jesus on the phone,
But Ol' Milwaukee's Best is my best friend.
-----------
mabshoff
On Dec 4, 9:33 pm, "Justin C. Walker" <jus...@mac.com> wrote:
> On Dec 3, 2007, at 23:27 , William Stein wrote:
>
>
>
> > Hello folks,
>
> > Sage 2.8.15 has been released. It is available at
>
> > http://sagemath.org/download.html
>
> Built and tested w/o errors on Mac OS X, as follows, both with
> "parallel make":
>
> 10.4.11 (Dual Quad-Core Xeon -j6):
> real 63m1.611s
> user 48m35.838s
> sys 25m26.978s
>
> All tests passed!
> Total time for all tests: 2366.0 seconds
>
> 10.5.1 (Core Duo, -j2):
> real 89m5.315s
> user 74m17.804s
> sys 16m57.508s
>
> All tests passed!
> Total time for all tests: 2552.2 seconds
>
> Still seeing mwrank crashing during the tests (10.5), but no comment
> in the logs.
i.e. input parameters for mwrank? Then I could take a look then, but
just shooting into the blue seems pointless.
> Justin
Cheers,
Michael
Justin C. Walker
On Dec 4, 2007, at 1:04 PM, mabshoff wrote:
> On Dec 4, 9:33 pm, "Justin C. Walker" <jus...@mac.com> wrote:
>> On Dec 3, 2007, at 23:27 , William Stein wrote:
>> Still seeing mwrank crashing during the tests (10.5), but no comment
>> in the logs.
>
> Any chance you could narrow this down to a specific doctests case,
> i.e. input parameters for mwrank? Then I could take a look then, but
> just shooting into the blue seems pointless.
I thought I batted that ball over to your court :-}
I know it happens during the 'tut.tex' doc test, and on a few more
way later in the tests; the latter whiz by quickly, so it's very hard
to peg it.
I will use the highly original trick of binary search :-}, and slice
and dice tut.tex to see if I can nail it. I'll try this tonight,
when I'm home.
Justin
--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Enhancement of the Director's Income
--------
When LuteFisk is outlawed,
Only outlaws will have LuteFisk
--------
mabshoff
On Dec 4, 10:30 pm, "Justin C. Walker" <jus...@mac.com> wrote:
> On Dec 4, 2007, at 1:04 PM, mabshoff wrote:
>
> > On Dec 4, 9:33 pm, "Justin C. Walker" <jus...@mac.com> wrote:
> >> On Dec 3, 2007, at 23:27 , William Stein wrote:
> >> Still seeing mwrank crashing during the tests (10.5), but no comment
> >> in the logs.
>
> > Any chance you could narrow this down to a specific doctests case,
> > i.e. input parameters for mwrank? Then I could take a look then, but
> > just shooting into the blue seems pointless.
>
> I thought I batted that ball over to your court :-}
>
than you think :)
Here is a session from sage.math with input "[0,0,1,-1,0]":
mabshoff@sage:/tmp/Work-mabshoff/release-cycles-2.9/sage-2.9.alpha0$ /
usr/local/valgrind-3.3.0svn-r6793/bin/valgrind --tool=memcheck --leak-
resolution=high ./local/bin/mwrank
==30271== Memcheck, a memory error detector.
==30271== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et
al.
==30271== Using LibVEX rev 1786, a library for dynamic binary
translation.
==30271== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
==30271== Using valgrind-3.3.0.SVN, a dynamic binary instrumentation
framework.
==30271== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et
al.
==30271== For more details, rerun with: -v
==30271==
Program mwrank: uses 2-descent (via 2-isogeny if possible) to
determine the rank of an elliptic curve E over Q, and list a
set of points which generate E(Q) modulo 2E(Q).
and finally saturate to obtain generating points on the curve.
For more details see the file mwrank.doc.
For details of algorithms see the author's book.
Please acknowledge use of this program in published work,
and send problems to john.c...@gmail.com.
Version compiled on Dec 4 2007 at 15:21:47 by GCC 4.1.2 20061115
(prerelease) (Debian 4.1.1-21)
using base arithmetic option NTL_ALL (NTL bigints and multiprecision
floating point)
Using NTL multiprecision floating point with 15 decimal places.
Enter curve: [0, 0, 1, -1, 0]
Curve [0,0,1,-1,0] : Basic pair: I=48, J=-432
disc=255744
2-adic index bound = 2
By Lemma 5.1(a), 2-adic index = 1
2-adic index = 1
One (I,J) pair
Looking for quartics with I = 48, J = -432
Looking for Type 2 quartics:
Trying positive a from 1 up to 1 (square a first...)
(1,0,-6,4,1) --trivial
Trying positive a from 1 up to 1 (...then non-square a)
Finished looking for Type 2 quartics.
Looking for Type 1 quartics:
Trying positive a from 1 up to 2 (square a first...)
(1,0,0,4,4) --nontrivial...(x:y:z) = (1 : 1 : 0)
Point = [0:0:1]
height = 0.0511114082399688
Rank of B=im(eps) increases to 1 (The previous point is on the egg)
Exiting search for Type 1 quartics after finding one which is globally
soluble.
Mordell rank contribution from B=im(eps) = 1
Selmer rank contribution from B=im(eps) = 1
Sha rank contribution from B=im(eps) = 0
Mordell rank contribution from A=ker(eps) = 0
Selmer rank contribution from A=ker(eps) = 0
Sha rank contribution from A=ker(eps) = 0
Rank = 1
Searching for points (bound = 8)...==30271== Conditional jump or move
depends on uninitialised value(s)
==30271== at 0x4C393CE: qsieve::sift0(long, long, long, int) (in /
tmp/Work-mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/
libmwrank.so)
==30271== by 0x4C397DA: qsieve::sift(long) (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C39E1A: qsieve::search() (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C2BF64: mw::search(NTL::RR, int, int) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4D2BA6C: two_descent::saturate(long) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x40162C: main (in /tmp/Work-mabshoff/release-
cycles-2.9/sage-2.9.alpha0/local/bin/mwrank)
==30271==
==30271== Conditional jump or move depends on uninitialised value(s)
==30271== at 0x4C38D35: qsieve::check_point(unsigned long, long,
long, long*, int) (in /tmp/Work-mabshoff/release-cycles-2.9/
sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C393E7: qsieve::sift0(long, long, long, int) (in /
tmp/Work-mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/
libmwrank.so)
==30271== by 0x4C397DA: qsieve::sift(long) (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C39E1A: qsieve::search() (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C2BF64: mw::search(NTL::RR, int, int) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4D2BA6C: two_descent::saturate(long) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x40162C: main (in /tmp/Work-mabshoff/release-
cycles-2.9/sage-2.9.alpha0/local/bin/mwrank)
==30271==
==30271== Conditional jump or move depends on uninitialised value(s)
==30271== at 0x4C38D5E: qsieve::check_point(unsigned long, long,
long, long*, int) (in /tmp/Work-mabshoff/release-cycles-2.9/
sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C393E7: qsieve::sift0(long, long, long, int) (in /
tmp/Work-mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/
libmwrank.so)
==30271== by 0x4C397DA: qsieve::sift(long) (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C39E1A: qsieve::search() (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C2BF64: mw::search(NTL::RR, int, int) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4D2BA6C: two_descent::saturate(long) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x40162C: main (in /tmp/Work-mabshoff/release-
cycles-2.9/sage-2.9.alpha0/local/bin/mwrank)
==30271==
==30271== Conditional jump or move depends on uninitialised value(s)
==30271== at 0x4C38D66: qsieve::check_point(unsigned long, long,
long, long*, int) (in /tmp/Work-mabshoff/release-cycles-2.9/
sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C393E7: qsieve::sift0(long, long, long, int) (in /
tmp/Work-mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/
libmwrank.so)
==30271== by 0x4C397DA: qsieve::sift(long) (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C39E1A: qsieve::search() (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C2BF64: mw::search(NTL::RR, int, int) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4D2BA6C: two_descent::saturate(long) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x40162C: main (in /tmp/Work-mabshoff/release-
cycles-2.9/sage-2.9.alpha0/local/bin/mwrank)
==30271==
==30271== Conditional jump or move depends on uninitialised value(s)
==30271== at 0x4C391AC: qsieve::check_point(unsigned long, long,
long, long*, int) (in /tmp/Work-mabshoff/release-cycles-2.9/
sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C393E7: qsieve::sift0(long, long, long, int) (in /
tmp/Work-mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/
libmwrank.so)
==30271== by 0x4C397DA: qsieve::sift(long) (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C39E1A: qsieve::search() (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C2BF64: mw::search(NTL::RR, int, int) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4D2BA6C: two_descent::saturate(long) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x40162C: main (in /tmp/Work-mabshoff/release-
cycles-2.9/sage-2.9.alpha0/local/bin/mwrank)
==30271==
==30271== Conditional jump or move depends on uninitialised value(s)
==30271== at 0x4C391ED: qsieve::check_point(unsigned long, long,
long, long*, int) (in /tmp/Work-mabshoff/release-cycles-2.9/
sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C393E7: qsieve::sift0(long, long, long, int) (in /
tmp/Work-mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/
libmwrank.so)
==30271== by 0x4C397DA: qsieve::sift(long) (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C39E1A: qsieve::search() (in /tmp/Work-mabshoff/
release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4C2BF64: mw::search(NTL::RR, int, int) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x4D2BA6C: two_descent::saturate(long) (in /tmp/Work-
mabshoff/release-cycles-2.9/sage-2.9.alpha0/local/lib/libmwrank.so)
==30271== by 0x40162C: main (in /tmp/Work-mabshoff/release-
cycles-2.9/sage-2.9.alpha0/local/bin/mwrank)
done:
found points of rank 1
and regulator 0.0511114082399688
Processing points found during 2-descent...done:
now regulator = 0.0511114082399688
Saturating (bound = 100)...done:
points were already saturated.
Generator 1 is [0:-1:1]; height 0.0511114082399688
Regulator = 0.0511114082399688
The rank and full Mordell-Weil basis have been determined
unconditionally.
> I know it happens during the 'tut.tex' doc test, and on a few more
> way later in the tests; the latter whiz by quickly, so it's very hard
> to peg it.
>
> I will use the highly original trick of binary search :-}, and slice
> and dice tut.tex to see if I can nail it. I'll try this tonight,
> when I'm home.
>
> Justin
Cheers,
Michael
Andrzej Giniewicz
I've seen that R moved from experimental to optional, now as
r-2.6.1.p6, tryied it but got:
sage: import rpy
---------------------------------------------------------------------------
<type 'exceptions.AttributeError'> Traceback (most recent call
last)
/home/giniu/<ipython console> in <module>()
/opt/sage/local/lib/python2.5/site-packages/rpy.py in <module>()
171
172 # The new exception
--> 173 RException = _rpy.RException
174
175 # I/O setters
<type 'exceptions.AttributeError'>: 'module' object has no attribute
'RException'
that can be known issue but I decided I will report... :)
best regards,
Andrzej.
William Stein
>
> Hi,
>
> I've seen that R moved from experimental to optional, now as
> r-2.6.1.p6, tryied it but got:
>
> sage: import rpy
> ---------------------------------------------------------------------------
> <type 'exceptions.AttributeError'> Traceback (most recent call
> last)
>
> /home/giniu/<ipython console> in <module>()
>
> /opt/sage/local/lib/python2.5/site-packages/rpy.py in <module>()
> 171
> 172 # The new exception
> --> 173 RException = _rpy.RException
> 174
> 175 # I/O setters
>
> <type 'exceptions.AttributeError'>: 'module' object has no attribute
> 'RException'
>
> that can be known issue but I decided I will report... :)
Thanks. However:
(1) What operating system are you using exactly, and what gcc version?
(2) Could you send the build log for building R (i.e., the end of
SAGE_ROOT/install.log)?
(3) If you type
sage: !R
what happens?
--William
Andrzej Giniewicz
On 10 Gru, 19:57, "William Stein" <wst...@gmail.com> wrote:
> On Dec 10, 2007 10:50 AM, Andrzej Giniewicz <ggi...@gmail.com> wrote:
>
>
>
>
>
> > Hi,
>
> > I've seen that R moved from experimental to optional, now as
> > r-2.6.1.p6, tryied it but got:
>
> > sage: import rpy
> > ---------------------------------------------------------------------------
> > <type 'exceptions.AttributeError'> Traceback (most recent call
> > last)
>
> > /home/giniu/<ipython console> in <module>()
>
> > /opt/sage/local/lib/python2.5/site-packages/rpy.py in <module>()
> > 171
> > 172 # The new exception
> > --> 173 RException = _rpy.RException
> > 174
> > 175 # I/O setters
>
> > <type 'exceptions.AttributeError'>: 'module' object has no attribute
> > 'RException'
>
> > that can be known issue but I decided I will report... :)
>
> Thanks. However:
> (1) What operating system are you using exactly, and what gcc version?
[giniu@ginland ~]$ gcc --v
Using built-in specs.
Target: i686-pc-linux-gnu
Configured with: ../configure --prefix=/usr --enable-shared --enable-
languages=c,c++,objc --enable-threads=posix --enable-__cxa_atexit --
disable-multilib --libdir=/usr/lib --libexecdir=/usr/lib --enable-
clocale=gnu --disable-libstdcxx-pch --with-tune=generic
Thread model: posix
gcc version 4.2.2
That's current Arch Linux, kernel 2.6.23.9 (stock distribution kernel)
and gLibc 2.7, my machine is 32bit Athlon Barton, exactly it's:
[giniu@ginland ~]$ cat /proc/cpuinfo
processor : 0
vendor_id : AuthenticAMD
cpu family : 6
model : 10
model name : AMD Athlon(tm) XP 2600+
stepping : 0
cpu MHz : 2091.122
cache size : 256 KB
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 1
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 mmx fxsr sse syscall mmxext 3dnowext 3dnow up ts
bogomips : 4186.91
clflush size : 32
> (2) Could you send the build log for building R (i.e., the end of
> SAGE_ROOT/install.log)?
http://giniu.ravenlord.ws/install.log - I renamed old log and did sage
-f r-2.6.1.p6 to be sure only needed lines are included
> (3) If you type
> sage: !R
> what happens?
it mostly works...
> --William
cheers,
Andrzej.
William Stein
> On 10 Gru, 19:57, "William Stein" <wst...@gmail.com> wrote:
> > On Dec 10, 2007 10:50 AM, Andrzej Giniewicz <ggi...@gmail.com> wrote:
> >
> >
> >
> >
> >
> > > Hi,
> >
> > > I've seen that R moved from experimental to optional, now as
> > > r-2.6.1.p6, tryied it but got:
> >
> > > sage: import rpy
> > > ---------------------------------------------------------------------------
> > > <type 'exceptions.AttributeError'> Traceback (most recent call
> > > last)
> >
> > > /home/giniu/<ipython console> in <module>()
> >
> > > /opt/sage/local/lib/python2.5/site-packages/rpy.py in <module>()
> > > 171
> > > 172 # The new exception
> > > --> 173 RException = _rpy.RException
> > > 174
> > > 175 # I/O setters
> >
> > > <type 'exceptions.AttributeError'>: 'module' object has no attribute
> > > 'RException'
> >
> > > that can be known issue but I decided I will report... :)
> >
> > Thanks. However:
> > (1) What operating system are you using exactly, and what gcc version?
>
> to be most specific...
Alright, I'm pretty stumped so far. what happens if you
just edit
/opt/sage/local/lib/python2.5/site-packages/rpy.py
and put a # at the beginning of the line
RException = _rpy.RException
and try again? I'm just curious.
Something is really weird, since for all my installs the context for the code
you list above is:
# Three new exceptions
# base exception
RPyException = _rpy.RPy_Exception;
# R <-> Python conversion exception
RPyTypeConversionException = _rpy.RPy_TypeConversionException;
# Exception raised by R
RPyRException = _rpy.RPy_RException
# for backwards compatibility
RException = RPyException
I wonder why your code looks totally different, why you have
# The new exception
RException = _rpy.RException
That code doesn't even appear in my rpy.py.
--
Andrzej Giniewicz
installed from -experimental messed something up, and it doesn't
update this file so maybe it's old one?... this could explain why it
looks different... revision of this file is quite old, that's Id tag:
rpy.py 342 2007-02-20 16:41:47Z warnes... commenting this line out
result in:
sage: from rpy import *
RPy version 1.0.1 [R version 2.6.1 (2007-11-26)]
I will remove this file, make sure write permission on all files are
ok and rebuild R spkg - I will be back with results in minutes...
Andrzej Giniewicz
so I removed this file, and it is now never... well... seems that at
switch from experimental to optional something went wrong on my local
machine... now it says:
sage: import rpy
sage: rpy.r
...
/opt/sage/local/lib/python2.5/site-packages/rpy.py in __repr__(self)
321
322 def __repr__(self):
--> 323 Rver = self.__getitem__('R_version_string')
324 return "RPy version %s [%s]" % (rpy_version, Rver)
325
/opt/sage/local/lib/python2.5/site-packages/rpy.py in
__getitem__(self, name)
304 def __getitem__(self, name):
305 # use r's 'get' function here, because the rpy one
only handles functions!
--> 306 obj = self.__dict__[name] = self.__dict__.get(name,
self.get(name))
307 return obj
308
<class 'rpy.RPy_RException'>: Error in function (x, pos = -1, envir =
as.environment(pos), mode = "any", :
variable "R_version_string" was not found
I remember I had same problem with experimental, I had to change
underscore to dot in name, and it was also on RPy mailing list for few
people... anyway I don't know if this is still some remaining part of
old version, or new... I'm going to build clean sage and then get this
package... will report back when it will be ready but it will take
some time...
sorry for troubles, didn't thought it can be old-file-problem,
A.
William Stein
I'm sorry for the troubles you're having, and greatly appreciate
that your testing the R spkg. That rpy doesn't overwrite
old files, etc., is something I'll have to keep in mind when we make
new spkg's that include new versions of R and rpy -- we'll have
to be careful to delete the old rpy files manually.
-- William
Andrzej Giniewicz
no problem, whole pleasure on my side :)
> That rpy doesn't overwrite
> old files, etc., is something I'll have to keep in mind when we make
> new spkg's that include new versions of R and rpy -- we'll have
> to be careful to delete the old rpy files manually.
then installed r-2.6.1.p6, this ensures fresh environment for R...
unfortuneatlly I get:
sage: import rpy
sage: rpy.r
<class 'rpy.RPy_RException'> Traceback (most recent call
/home/giniu/<ipython console> in <module>()
__call__(self,
arg)
521
522 # and now call a possibly user-defined print
mechanism
--> 523 manipulated_val = self.display(arg)
524
525 # user display hooks can change the variable to be
stored in
/opt/sage/local/lib/python2.5/site-packages/IPython/Prompts.py in
_display(self,
arg)
545 """
546
--> 547 return self.shell.hooks.result_display(arg)
548
549 # Assign the default display method:
/opt/sage/local/lib/python2.5/site-packages/IPython/hooks.py in
__call__(self, *
args, **kw)
132 #print "prio",prio,"cmd",cmd #dbg
133 try:
--> 134 ret = cmd(*args, **kw)
135 return ret
136 except ipapi.TryNext, exc:
/opt/sage/local/lib/python2.5/site-packages/IPython/hooks.py in
result_display(s
elf, arg)
160
161 if self.rc.pprint:
--> 162 out = pformat(arg)
163 if '\n' in out:
164 # So that multi-line strings line up with the left
column of
/opt/sage/local/lib/python2.5/pprint.py in pformat(self, object)
109 def pformat(self, object):
110 sio = _StringIO()
--> 111 self._format(object, sio, 0, 0, {}, 0)
112 return sio.getvalue()
113
/opt/sage/local/lib/python2.5/pprint.py in _format(self, object,
stream, indent,
allowance, context, level)
127 self._readable = False
128 return
--> 129 rep = self._repr(object, context, level - 1)
130 typ = _type(object)
131 sepLines = _len(rep) > (self._width - 1 - indent -
allowance)
/opt/sage/local/lib/python2.5/pprint.py in _repr(self, object,
context, level)
193 def _repr(self, object, context, level):
194 repr, readable, recursive = self.format(object,
context.copy(),
--> 195 self._depth,
level)
196 if not readable:
197 self._readable = False
/opt/sage/local/lib/python2.5/pprint.py in format(self, object,
context, maxleve
ls, level)
205 and whether the object represents a recursive
construct.
206 """
--> 207 return _safe_repr(object, context, maxlevels, level)
208
209
/opt/sage/local/lib/python2.5/pprint.py in _safe_repr(object, context,
maxlevels
, level)
290 return format % _commajoin(components), readable,
recursive
291
--> 292 rep = repr(object)
293 return rep, (rep and not rep.startswith('<')), False
294
/opt/sage/local/lib/python2.5/site-packages/rpy.py in __repr__(self)
321
322 def __repr__(self):
--> 323 Rver = self.__getitem__('R_version_string')
324 return "RPy version %s [%s]" % (rpy_version, Rver)
325
/opt/sage/local/lib/python2.5/site-packages/rpy.py in
__getitem__(self, name)
304 def __getitem__(self, name):
305 # use r's 'get' function here, because the rpy one
only handles
functions!
--> 306 obj = self.__dict__[name] = self.__dict__.get(name,
self.get(nam
e))
307 return obj
308
<class 'rpy.RPy_RException'>: Error in function (x, pos = -1, envir =
as.environ
ment(pos), mode = "any", :
variable "R_version_string" was not found
after I changed:
def __repr__(self):
def __repr__(self):
sage: import rpy
sage: rpy.r
do this in notebook:
=============================================
from rpy import *
r.png("test.png", bg="white", width=int(400), height=int(400))
r.hist(r.rnorm(1000))
r.dev_off()
=============================================
but got very strange result... is there some changes in workflow to
work with R from Sage? I got image in background AND whole lot of
numbers on top... I put it there: http://giniu.ravenlord.ws/test.png
also one question - as it's possible to install new packages from R
console, would new commands be somehow accessible from Sage or it
would need rebuild of RPy / change in Sage code?
Cheers,
Andrzej.
>
> -- William
Marshall Hampton
I'm not very familiar with R and rpy, but in reading the rpy
documentation they implied that if you install optional R components
you do _not_ have to rebuild rpy...but I suppose someone should verify/
test that.
Marshall Hampton
Andrzej Giniewicz
install any package... take a look at this:
gcc -std=gnu99 -I/opt/sage/local/lib/r//include -I/opt/sage/local/lib/
r//include -I/usr/local/include WARNING: ignoring environment value
of R_HOME -fvisibility=hidden -fpic -I/opt/sage/local/include -L/opt/
sage/local/lib/ -c corStruct.c -o corStruct.o
gcc: WARNING:: No such file or directory
gcc: ignoring: No such file or directory
gcc: environment: No such file or directory
gcc: value: No such file or directory
gcc: of: No such file or directory
gcc: R_HOME: No such file or directory
make: *** [corStruct.o] Error 1
this actually stops any addon R library installation... I got that
running R from Sage, using !R and typing install.packages("MASS",
dependencies=T) - there are more of those of course, for almost
every .c file in libraries... after commenting out first few lines in
local/bin/R and local/lib/r/bin/R - warning was no longer generated
and thus I was able to install packages... (I think those can be
commented because variables set and checked there are overwritten in
"sagehack" just below... this almost allowed me to build packages,
because one failed (it works on my plain R install, sage-fortran
wasn't able to compile one file - it was library "Hmisc" that failed:
sage_fortran -fpic -g -O2 -c largrec.f -o largrec.o
In file largrec.f:27
DO xl=xlim(1),xlim(2)-width,xinc
1
Error: Loop variable at (1) must be a scalar INTEGER
In file largrec.f:28
DO yl=ylim(1),ylim(2)-height,yinc
1
Error: Loop variable at (1) must be a scalar INTEGER
In file largrec.f:29
DO xr=xl+width,xlim(2),xinc
1
Error: Loop variable at (1) must be a scalar INTEGER
In file largrec.f:30
DO yu=yl+height,ylim(2),yinc
1
Error: Loop variable at (1) must be a scalar INTEGER
make: *** [largrec.o] Error 1
is this sage_fortran problem or package problem but it works on system
compiler...
anyway I installed other package (tseries) and was able to use
functions from (from R console, Sage console and notebook), just auto-
compl. worked for those functions after they were called for the first
time not before...
On Dec 12, 2007 2:35 AM, Marshall Hampton <hamp...@gmail.com> wrote:
>
> Hi,
>
> I'm not very familiar with R and rpy, but in reading the rpy
> documentation they implied that if you install optional R components
> you do _not_ have to rebuild rpy...but I suppose someone should verify/
> test that.
>
> Marshall Hampton
>
Andrzej.
William Stein
Excellent. Many thanks for your report. We'll incorporate your fixes
into sage: http://trac.sagemath.org/sage_trac/ticket/1476
> On Dec 12, 2007 2:35 AM, Marshall Hampton <hamp...@gmail.com> wrote:
> >
> > Hi,
> >
> > I'm not very familiar with R and rpy, but in reading the rpy
> > documentation they implied that if you install optional R components
> > you do _not_ have to rebuild rpy...but I suppose someone should verify/
> > test that.
> >
> > Marshall Hampton
> >
>
> cheers,
> Andrzej.
>
>
> >
>
--