sage-5.2.rc0 released

[Jeroen Demeyer]

Dear Sage lovers,

We're releasing Sage 5.2.rc0.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.2.rc0/sage-5.2.rc0.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.2.rc0/sage-5.2.rc0/

The source and upgrade path can also be found on the mirror network
(you might need to wait a while before the mirrors are synchronized):

http://www.sagemath.org/download-latest.html


Please build, test, and report! We'd love to hear about your
experiences with this release.

== Tickets ==

* We closed 86 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.2.rc0/tickets.html

Closed tickets:

#876: Implement or wrap Braid Groups [Reviewed by Karl-Dieter Crisman]
#8393: bring plot3d.py to 100% coverage [Reviewed by Karl-Dieter Crisman]
#10144: Update plot.py to 100% coverage [Reviewed by Karl-Dieter Crisman]
#10694: bug with plot [Reviewed by Karl-Dieter Crisman]
#11953: Marshall Hampton, John Palmieri: Upgrade optional package
biopython to version 1.60 [Reviewed by Marshall Hampton, John Palmieri]
#13205: make LP return bounds on variables [Reviewed by Dmitrii Pasechnik]
#13207: Please consider updating to gfan 0.5 [Reviewed by Marshall Hampton]

Merged in sage-5.2.rc0:

#10607: Marshall Hampton, John Palmieri: Update phcpack to latest verson
[Reviewed by Marshall Hampton, John Palmieri]
#11563: Nicolas M. Thiéry: Make lrcalc a standard package [Reviewed by
Anne Schilling, Jeroen Demeyer, John Palmieri]
#11996: Johan Bosman: Bug in LaTeX representation of subgroups of
permutation groups [Reviewed by Samuel Gonshaw]
#12343: Luis Felipe Tabera Alonso: Cleanup unexisting methods after
#10263 [Reviewed by André Apitzsch]
#12925: Nicolas M. Thiéry, Hugh Thomas: Thematic tutorial on
combinatorics [Reviewed by Hugh Thomas, Nicolas M. Thiéry, Timothy Walsh]
#13073: Birk Eisermann: recognition of weakly chordal graphs [Reviewed
by Nathann Cohen,Birk Eisermann]
#13088: Frédéric Chapoton: implement the Paley graphs [Reviewed by
Nathann Cohen]
#13109: Volker Braun: Rewrite deprecation to use trac ticket numbers
[Reviewed by John Palmieri, Karl-Dieter Crisman]
#13146: David Roe: Removing tabs in .rst, .tex and .pxi files [Reviewed
by Keshav Kini, André Apitzsch, Jeroen Demeyer]
#13193: Benjamin Jones: erf evaluation is wrong along imaginary axis
[Reviewed by Karl-Dieter Crisman]
#13220: John Palmieri: bug in morphisms of chain complexes [Reviewed by
Marshall Hampton]

[Andrey Novoseltsev]

I've successfully complied and started Sage-5.2.rc0 without any
patches applied, Linux Mint 11 64-bit on AMD CPU.

Then I have started notebook and it allowed user registration.

I had this issue yesterday when I tried sagenb-0.10.1 on top of
Sage-5.2.beta2: I have turned off registration manually, saved it, and
checked that the registration link was gone from the start page. Yet
when I started rc0 today the first time it was back. I turned it off
again and restarted Sage and the notebook server - everything is fine
now, so it seems like a one-time issue, but I think it is a very
serious security bug - users who were using private servers to connect
to them from other machines suddenly will be opening these machines to
anyone who decides to register.

Andrey

[Andrey Novoseltsev]

Oops, my second attempt before was with default sage.

If I restart the notebook server under Sage-5.2.rc0 without anything,
then user registration is enabled every time - turning it off is not
saved between sessions.

Andrey

[leif]

Jeroen Demeyer wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.2.rc0.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.2.rc0/sage-5.2.rc0.tar
>
> Upgrade path:
>
> http://boxen.math.washington.edu/home/release/sage-5.2.rc0/sage-5.2.rc0/

Why do many spkgs frequently have newer timestamps although they haven't
been updated (at least not "officially", [and w.r.t. the previous Sage
version])?


leif@sage$ ls -rtl /home/release/sage-5.2.rc0/sage-5.2.rc0/spkg/standard/
...
-rw-r--r-- 1 jdemeyer jdemeyer 26839452 2012-07-17 01:40 sagenb-0.9.0.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 549881 2012-07-17 01:40 cython-0.17pre.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 2654114 2012-07-17 01:40
mercurial-2.2.2.p0.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 3825991 2012-07-17 01:41 mpir-2.4.0.p6.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 1265442 2012-07-17 01:41 mpfr-3.1.0.p2.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 741141 2012-07-17 01:41 ecm-6.3.p8.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 151230 2012-07-17 01:41 zn_poly-0.9.p9.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 1845671 2012-07-17 01:41 polybori-0.8.2.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 42 2012-07-17 04:49 VERSION.txt
-rw-r--r-- 1 jdemeyer jdemeyer 54608576 2012-07-17 04:51 sage-5.2.rc0.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 12219704 2012-07-17 04:51
extcode-5.2.rc0.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 1086948 2012-07-17 04:51
sage_scripts-5.2.rc0.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 287849 2012-07-17 04:51
sage_root-5.2.rc0.spkg
-rw-r--r-- 1 jdemeyer jdemeyer 43 2012-07-17 04:51 README.txt
-rwxr-xr-x 1 jdemeyer jdemeyer 175 2012-07-17 04:51 newest_version
-rw-r--r-- 1 jdemeyer jdemeyer 23077 2012-07-17 04:51 deps


That's quite inconvenient when rsyncing from some previous release.

It would IMHO make more sense to create hard links for spkgs (at least
for those that aren't new) anyway.


-leif

--
() The ASCII Ribbon Campaign
/\ Help Cure HTML E-Mail

[leif]

More precisely, it's not just the timestamps, but e.g.

leif@sage:/home/release$ md5sum
sage-*/sage-*/spkg/standard/mpir-2.4.0.p6.spkg
018ed3168f251a01c39139bff641c55b
sage-5.2.beta1/sage-5.2.beta1/spkg/standard/mpir-2.4.0.p6.spkg
fecfbb10883757d1e68ae588f21a80dd
sage-5.2.rc0/sage-5.2.rc0/spkg/standard/mpir-2.4.0.p6.spkg
leif@sage:/home/release$ md5sum
sage-*/sage-*/spkg/standard/mpfr-3.1.0.p2.spkg
b5c212a9163d6d90fdc95ca5c4c6067b
sage-5.2.beta1/sage-5.2.beta1/spkg/standard/mpfr-3.1.0.p2.spkg
4096986f7d919970533aac70d422135a
sage-5.2.rc0/sage-5.2.rc0/spkg/standard/mpfr-3.1.0.p2.spkg


Same for the other spkgs listed above.

[Michael Welsh]

On 18/07/2012, at 12:12 AM, Jeroen Demeyer wrote:
>
> Please build, test, and report! We'd love to hear about your
> experiences with this release.

All tests passed (ptestlong) on OS X 10.7.4 Quad Core i7

[Keshav Kini]

leif <not.r...@online.de> writes:
> More precisely, it's not just the timestamps, but e.g.
>
> leif@sage:/home/release$ md5sum
> sage-*/sage-*/spkg/standard/mpir-2.4.0.p6.spkg
> 018ed3168f251a01c39139bff641c55b
> sage-5.2.beta1/sage-5.2.beta1/spkg/standard/mpir-2.4.0.p6.spkg
> fecfbb10883757d1e68ae588f21a80dd
> sage-5.2.rc0/sage-5.2.rc0/spkg/standard/mpir-2.4.0.p6.spkg
> leif@sage:/home/release$ md5sum
> sage-*/sage-*/spkg/standard/mpfr-3.1.0.p2.spkg
> b5c212a9163d6d90fdc95ca5c4c6067b
> sage-5.2.beta1/sage-5.2.beta1/spkg/standard/mpfr-3.1.0.p2.spkg
> 4096986f7d919970533aac70d422135a
> sage-5.2.rc0/sage-5.2.rc0/spkg/standard/mpfr-3.1.0.p2.spkg

Jeroen's merger script unpacks SPKGs and fiddles with their hg repos,
doing stuff like committing uncommitted changes, and making the dreaded
"Added tag foo for changeset bar" commit. This is redone for every
development release, so various data is different, thus the SPKG has a
different MD5 hash.

[1] keshav@sage /tmp $ diff -ur mpfr-from-beta1 mpfr-from-rc0
diff -ur mpfr-from-beta1/.hg/cache/branchheads mpfr-from-rc0/.hg/cache/branchheads
--- mpfr-from-beta1/.hg/cache/branchheads 2012-07-13 04:48:17.000000000 -0700
+++ mpfr-from-rc0/.hg/cache/branchheads 2012-07-17 01:41:19.000000000 -0700
@@ -1,2 +1,2 @@
-a7cac21502a04961c60e65fb10c0e98c696b5c0c 35
-a7cac21502a04961c60e65fb10c0e98c696b5c0c default
+19a0be7ee5754f5f3d2cc417383b9155e155c85a 35
+19a0be7ee5754f5f3d2cc417383b9155e155c85a default
diff -ur mpfr-from-beta1/.hg/cache/tags mpfr-from-rc0/.hg/cache/tags
--- mpfr-from-beta1/.hg/cache/tags 2012-07-13 04:48:16.000000000 -0700
+++ mpfr-from-rc0/.hg/cache/tags 2012-07-17 20:52:33.291164295 -0700
@@ -1,7 +1,8 @@
-34 9c2303a2bd33af682d60e944cf30e4014fd4046a 4232ea72da62646c6085e1a8bb54d3b59b3dfe08
+35 19a0be7ee5754f5f3d2cc417383b9155e155c85a f0a49204d83b56e1a1e3b28115654684062f55c4

b9faebc37a62ab557543b26b27e3747429672552 mpfr-3.1.0.p1
834f2c4e0347c2e4249d94188203d93cea44d92a mpfr-3.1.0.p0
+6de3caa7cb04a635b505ec2bbdeb6a54b1a750fc mpfr-3.1.0.p2
ad149c890ee193fbe7d2fdbebf94dee20eb6a612 mpfr-3.1.0
c24b1e8f4ba1fce31bb2ea48bb069bedaebe3d32 mpfr-2.4.2.p2
8094e7388f5bae4105a4e3ff49967fd246817559 mpfr-2.4.2.p1
Binary files mpfr-from-beta1/.hg/dirstate and mpfr-from-rc0/.hg/dirstate differ
diff -ur mpfr-from-beta1/.hg/last-message.txt mpfr-from-rc0/.hg/last-message.txt
--- mpfr-from-beta1/.hg/last-message.txt 2012-07-13 04:48:17.000000000 -0700
+++ mpfr-from-rc0/.hg/last-message.txt 2012-07-17 01:41:19.000000000 -0700
@@ -1 +1 @@
-Added tag mpfr-3.1.0.p2 for changeset 9c2303a2bd33
\ No newline at end of file
+Added tag mpfr-3.1.0.p2 for changeset 6de3caa7cb04
\ No newline at end of file
Binary files mpfr-from-beta1/.hg/store/00changelog.i and mpfr-from-rc0/.hg/store/00changelog.i differ
Binary files mpfr-from-beta1/.hg/store/00manifest.i and mpfr-from-rc0/.hg/store/00manifest.i differ
Binary files mpfr-from-beta1/.hg/store/data/.hgtags.i and mpfr-from-rc0/.hg/store/data/.hgtags.i differ
Binary files mpfr-from-beta1/.hg/undo.dirstate and mpfr-from-rc0/.hg/undo.dirstate differ
diff -ur mpfr-from-beta1/.hgtags mpfr-from-rc0/.hgtags
--- mpfr-from-beta1/.hgtags 2012-07-13 04:48:17.000000000 -0700
+++ mpfr-from-rc0/.hgtags 2012-07-17 01:41:19.000000000 -0700
@@ -4,4 +4,4 @@
ad149c890ee193fbe7d2fdbebf94dee20eb6a612 mpfr-3.1.0
834f2c4e0347c2e4249d94188203d93cea44d92a mpfr-3.1.0.p0
b9faebc37a62ab557543b26b27e3747429672552 mpfr-3.1.0.p1
-9c2303a2bd33af682d60e944cf30e4014fd4046a mpfr-3.1.0.p2
+6de3caa7cb04a635b505ec2bbdeb6a54b1a750fc mpfr-3.1.0.p2

-Keshav

----
Join us in #sagemath on irc.freenode.net !

[Keshav Kini]

Keshav Kini <kesha...@gmail.com> writes:
> Jeroen's merger script unpacks SPKGs and fiddles with their hg repos,
> doing stuff like committing uncommitted changes, and making the dreaded
> "Added tag foo for changeset bar" commit. This is redone for every
> development release, so various data is different, thus the SPKG has a
> different MD5 hash.

Actually it's not just the .hgtags commit; Jeroen is also recommitting
his latest change to the SPKG, for some reason. He didn't actually do
anything differently the two times, though:

[1] keshav@sage /tmp $ diff -u <(hg -R mpfr-from-beta1 log -p -l1 -r -2) <(hg -R mpfr-from-rc0 log -p -l1 -r -2)
--- /dev/fd/63 2012-07-17 21:13:23.403040131 -0700
+++ /dev/fd/62 2012-07-17 21:13:23.403040131 -0700
@@ -1,7 +1,7 @@
-changeset: 34:9c2303a2bd33
+changeset: 34:6de3caa7cb04
tag: mpfr-3.1.0.p2
user: Jeroen Demeyer <jdem...@cage.ugent.be>
-date: Fri Jul 13 11:48:16 2012 +0000
+date: Tue Jul 17 08:41:18 2012 +0000
summary: Trac #12751: mpfr-3.1.0.p2 (Jeroen Demeyer, 28 May 2012)

diff --git a/SPKG.txt b/SPKG.txt

[Jeroen Demeyer]

On 2012-07-18 06:14, Keshav Kini wrote:
> Actually it's not just the .hgtags commit; Jeroen is also recommitting
> his latest change to the SPKG, for some reason.

That's a bug, this shouldn't happen anymore.

[Jeroen Demeyer]

On 2012-07-18 05:57, Keshav Kini wrote:
> Jeroen's merger script unpacks SPKGs and fiddles with their hg repos,
> doing stuff like committing uncommitted changes, and making the dreaded
> "Added tag foo for changeset bar" commit. This is redone for every
> development release, so various data is different, thus the SPKG has a
> different MD5 hash.

At the very least, I unpack and repack the spkg. This is needed to deal
with subtle incompatibilities in tar formats (we had an issue before
where a tarfile created on OS X unpacked badly on some other system).

Then, I do indeed add the hg tag. I also commit changes, but this
should be done by the spkg author (I now check for this).

[Justin C. Walker]

On Jul 17, 2012, at 05:12 , Jeroen Demeyer wrote:

> Dear Sage lovers,
>
> We're releasing Sage 5.2.rc0.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.2.rc0/sage-5.2.rc0.tar

On Mac OS X:
10.6.8 (Dual 6-core Xeons): built w/o problems; all tests passed!
10.7.4 (Quad-core Core i7): built w/o problems; all tests passed!

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.
-----------

[leif]

Keshav Kini wrote:
> leif<not.r...@online.de> writes:
>> More precisely, it's not just the timestamps, but e.g.
>>
>> leif@sage:/home/release$ md5sum
>> sage-*/sage-*/spkg/standard/mpir-2.4.0.p6.spkg
>> 018ed3168f251a01c39139bff641c55b
>> sage-5.2.beta1/sage-5.2.beta1/spkg/standard/mpir-2.4.0.p6.spkg
>> fecfbb10883757d1e68ae588f21a80dd
>> sage-5.2.rc0/sage-5.2.rc0/spkg/standard/mpir-2.4.0.p6.spkg
>> leif@sage:/home/release$ md5sum
>> sage-*/sage-*/spkg/standard/mpfr-3.1.0.p2.spkg
>> b5c212a9163d6d90fdc95ca5c4c6067b
>> sage-5.2.beta1/sage-5.2.beta1/spkg/standard/mpfr-3.1.0.p2.spkg
>> 4096986f7d919970533aac70d422135a
>> sage-5.2.rc0/sage-5.2.rc0/spkg/standard/mpfr-3.1.0.p2.spkg
>
> Jeroen's merger script unpacks SPKGs and fiddles with their hg repos,
> doing stuff like committing uncommitted changes, and making the dreaded
> "Added tag foo for changeset bar" commit. This is redone for every
> development release, so various data is different, thus the SPKG has a
> different MD5 hash.

Yep, I was thinking of such, but it doesn't make sense to repackage
already "finalized" spkgs for each and every [devel] release.

It also wastes a lot of disk space btw., hence I suggested using hard
links (which transparently work with 'tar' or 'rsync').

[For "backward compatibility", that of course requires the patch level
of an spkg getting bumped if an spkg /really/ changes inbetween, e.g.
when it gets unmerged and a modified version later merged back in; but
that's reasonable anyway...]

[leif]

Well, that's pretty ok, and I don't mind if it's done *exactly once*,
the first time some spkg is officially /released/ (as opposed to
published on / via trac).

If a ticket with an spkg gets positive review and closed, the spkg
should get "finalized" and that copy stored somewhere [else].

[leif]

Justin C. Walker wrote:
>
> On Jul 17, 2012, at 05:12 , Jeroen Demeyer wrote:
>
>> Dear Sage lovers,
>>
>> We're releasing Sage 5.2.rc0.
>>
>> Source archive:
>>
>> http://boxen.math.washington.edu/home/release/sage-5.2.rc0/sage-5.2.rc0.tar
>
> On Mac OS X:
> 10.6.8 (Dual 6-core Xeons): built w/o problems; all tests passed!
> 10.7.4 (Quad-core Core i7): built w/o problems; all tests passed!

Same on Ubuntu 10.04.4 LTS x86_64 (GCC 4.4.3; ATLAS 3.10.0 from #10508
with SAGE_ATLAS_ARCH=base).

[Hugh Thomas]

Hi!

Sage 5.2.rc0 built successfully for me, under ubuntu 11.10 (oneiric), on a 32 bit machine, with processors Intel CPU U7300 @ 1.30GHz × 2. 

This is progress compared to beta1; I apparently had the same problem reported by a couple of others (Marshall, Martin).  In between I installed libssl-dev, which could be (part of?) why it's working now. 

I have a question about the notebook's behaviour on termination.  If I want to stop running the notebook, my understanding is that the right way to do that is to type ctrl-C.  If I do that in 5.2.rc0, I get the usual output followed by

*** glibc detected *** python: free(): invalid pointer: 0x01d9d770 ***
======= Backtrace: =========
/lib/i386-linux-gnu/libc.so.6(+0x6ff22)[0x8d4f22]
/lib/i386-linux-gnu/libc.so.6(+0x70bc2)[0x8d5bc2]
/lib/i386-linux-gnu/libc.so.6(cfree+0x6d)[0x8d8cad]
/home/hugh/sage-5.2.rc0/local/lib/libcsage.so(+0x7dad)[0x554dad]
/home/hugh/sage-5.2.rc0/local/lib/libcsage.so(sage_mpir_free+0x11)[0x554e30]
/home/hugh/sage-5.2.rc0/local/lib/libgmp.so.7(__gmpz_clear+0x2a)[0x264e9a]
/home/hugh/sage-5.2.rc0/local/lib/libgivaro.so.0(_ZN7IntegerD2Ev+0x1d)[0x3bf70d9]
/home/hugh/sage-5.2.rc0/local/lib/libgivaro.so.0(_ZN8RationalD2Ev+0x21)[0x3c013ad]
/lib/i386-linux-gnu/libc.so.6(+0x32981)[0x897981]
/lib/i386-linux-gnu/libc.so.6(+0x32a0d)[0x897a0d]
/lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xfb)[0x87e11b]
python[0x804852d]
======= Memory map: ========
<snip, it's fairly long; I can post it somewhere if it would be useful>
------------------------------------------------------------------------
Unhandled SIGABRT: An abort() occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off(). You might
want to run Sage under gdb with 'sage -gdb' to debug this.
Sage will now terminate.
------------------------------------------------------------------------
Aborted
True

But in fact, Sage does not terminate, it gives me a prompt and seems to be fine.  Nonetheless this doesn't sound entirely happy.  The phenomenon is reproducible. 

cheers,

Hugh

[Jeroen Demeyer]

On 2012-07-18 23:29, Hugh Thomas wrote:
> But in fact, Sage does not terminate, it gives me a prompt and seems to
> be fine. Nonetheless this doesn't sound entirely happy. The phenomenon
> is reproducible.

Is it reproducible in the sense that it occurs always or just more than
once?
It it reproducible only when you actually do something in the notebook
or also if you just start up the notebook and CTRL-C immediately?

[Hugh Thomas]

It always happens if I type control-C after starting the notebook. 

In particular, it happens if I just type notebook(), let it start the notebook up (which opens my browser), and then type ctrl-C without doing anything further. 

cheers,

Hugh



On Tuesday, July 17, 2012 9:12:10 PM UTC+9, Jeroen Demeyer wrote:

[Andrey Novoseltsev]

Here is what is happening to me:

novoselt@zv5000-lmde ~/sage/devel/sage-main $ sage
----------------------------------------------------------------------
| Sage Version 5.2.rc0, Release Date: 2012-07-17                     |
| Type "notebook()" for the browser-based notebook interface.        |
| Type "help()" for help.                                            |
----------------------------------------------------------------------
**********************************************************************
*                                                                    *
* Warning: this is a prerelease version, and it may be unstable.     *
*                                                                    *
**********************************************************************
sage: notebook()
The notebook files are stored in: sage_notebook.sagenb
**************************************************
*                                                *
* Open your web browser to http://localhost:8080 *
*                                                *
**************************************************
2012-07-19 08:16:42-0600 [-] Log opened.
2012-07-19 08:16:42-0600 [-] twistd 12.1.0 (/home/novoselt/sage-5.2.rc0/local/bin/python 2.7.3) starting up.
2012-07-19 08:16:42-0600 [-] reactor class: twisted.internet.epollreactor.EPollReactor.
2012-07-19 08:16:42-0600 [-] QuietSite starting on 8080
2012-07-19 08:16:42-0600 [-] Starting factory <__builtin__.QuietSite instance at 0x61c8440>
^C2012-07-19 08:16:51-0600 [-] Quitting all running worksheets...
2012-07-19 08:16:51-0600 [-] Saving notebook...
2012-07-19 08:16:51-0600 [-] Notebook cleanly saved.
2012-07-19 08:16:51-0600 [-] (TCP Port 8080 Closed)
2012-07-19 08:16:51-0600 [-] Stopping factory <__builtin__.QuietSite instance at 0x61c8440>
2012-07-19 08:16:51-0600 [-] Main loop terminated.
2012-07-19 08:16:51-0600 [-] Server Shut Down.
/home/novoselt/sage-5.2.rc0/local/lib/libcsage.so(print_backtrace+0x31)[0x7ffc1ba25c47]
/home/novoselt/sage-5.2.rc0/local/lib/libcsage.so(sigdie+0x14)[0x7ffc1ba25c79]
/home/novoselt/sage-5.2.rc0/local/lib/libcsage.so(sage_signal_handler+0x216)[0x7ffc1ba25856]
/lib/x86_64-linux-gnu/libpthread.so.0(+0xf030)[0x7ffc21935030]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x19)[0x7ffc20f90799]
/home/novoselt/sage-5.2.rc0/local/lib/libcsage.so(+0xad85)[0x7ffc1ba25d85]
/home/novoselt/sage-5.2.rc0/local/lib/libcsage.so(sage_mpir_free+0x1c)[0x7ffc1ba25e31]
/home/novoselt/sage-5.2.rc0/local/lib/libgivaro.so.0(_ZN7IntegerD2Ev+0x18)[0x7ffc08e30e9c]
/home/novoselt/sage-5.2.rc0/local/lib/libgivaro.so.0(_ZN8RationalD2Ev+0x1d)[0x7ffc08e3b47b]
/lib/x86_64-linux-gnu/libc.so.6(+0x36df2)[0x7ffc20f4cdf2]
/lib/x86_64-linux-gnu/libc.so.6(+0x36e45)[0x7ffc20f4ce45]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x104)[0x7ffc20f34eb4]
python[0x4006a1]

------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred in Sage.

This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off(). You might
want to run Sage under gdb with 'sage -gdb' to debug this.
Sage will now terminate.
------------------------------------------------------------------------

Segmentation fault
True
sage: 1 + 3
4
sage:

This does happen every time on this machine (8 years old notebook on Athlon64, 2Gb RAM, never had such issues before).

I have also opened
http://trac.sagemath.org/sage_trac/ticket/13270
for automatic reenabling of user registration.

Andrey

[bump]

sage-5.2.rc0 did not build for me on an Ubuntu machine that usually builds sage without trouble.
My install.log may be found at:

http://sporadic.stanford.edu/bump/install.log .

Dan

[leif]

Looks like

...
In file included from OpenSSL/crypto/crypto.h:17:0,
from OpenSSL/crypto/crypto.c:16:
OpenSSL/crypto/x509.h:17:25: fatal error: openssl/ssl.h: No such file or
directory
compilation terminated.
error: Setup script exited with error: command 'gcc' failed with exit
status 1
Error installing pyOpenSSL-0.12.tar.gz.

real 0m27.701s
user 0m14.520s
sys 0m2.630s
************************************************************************
Error installing package sagenb-0.9.0
************************************************************************

is the relevant part of this fairly long log... ;-)


Either install libssl-dev (with 'sudo apt-get install libssl-dev'), or
the optional OpenSSL spkg (with './sage -i openssl'), the latter not
requiring admin rights. Then resume the build by typing 'make' again.

See also previous posts in this thread (and the 5.2.beta1 thread IIRC).

[Tim Joseph Dumol]

--
You received this message because you are subscribed to the Google Groups "sage-release" group.
To post to this group, send email to sage-r...@googlegroups.com.
To unsubscribe from this group, send email to sage-release...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/sage-release?hl=en.

Built with no problems, and all (long) tests passed:

Linux timdumol-laptop-linux 3.4.4-2-ARCH #1 SMP PREEMPT Sun Jun 24 18:59:47 CEST 2012 x86_64 GNU/Linux

gcc 4.7.1

Intel(R) Core(TM) i5 CPU       M 460  @ 2.53GH

Yours,
Tim Dumol

[leif]

leif wrote:
> Justin C. Walker wrote:
>>
>> On Jul 17, 2012, at 05:12 , Jeroen Demeyer wrote:
>>
>>> Dear Sage lovers,
>>>
>>> We're releasing Sage 5.2.rc0.
>>>
>>> Source archive:
>>>
>>> http://boxen.math.washington.edu/home/release/sage-5.2.rc0/sage-5.2.rc0.tar
>>>
>>
>> On Mac OS X:
>> 10.6.8 (Dual 6-core Xeons): built w/o problems; all tests passed!
>> 10.7.4 (Quad-core Core i7): built w/o problems; all tests passed!
>
> Same on Ubuntu 10.04.4 LTS x86_64 (GCC 4.4.3; ATLAS 3.10.0 from #10508
> with SAGE_ATLAS_ARCH=base).

Same with FSF GCC 4.6.3, i.e., ptestlong passed.

With (FSF) GCC 4.7.0 and '-O3', building the R spkg fails as usual
(segfault when byte-compiling package "base"); '-O2' in contrast works,
and all tests passed.

(Building the R spkg also fails with GCC 4.7.1 [from Jeroen's new spkg]
and '-O3'. Probably a [GNU] compiler bug, but presumably hard to track
down.)

[leif]

leif wrote:
> With (FSF) GCC 4.7.0 and '-O3', building the R spkg fails as usual
> (segfault when byte-compiling package "base"); '-O2' in contrast works,
> and all tests passed.

[Ubuntu 10.04.4 LTS x86_64; R 2.14.0.p3]

Interestingly, using '-O3 -flto' works as well (while Simon King
reported [1] LTO did not work with the R spkg, although with GCC 4.6.3).

So this looks like a GCC bug.

> (Building the R spkg also fails with GCC 4.7.1 [from Jeroen's new spkg]
> and '-O3'. Probably a [GNU] compiler bug, but presumably hard to track
> down.)

Jeroen's optional GCC 4.7.1 spkg is available at #13150 [2] (needs
review btw.). As far as I know, it doesn't support using LTO, but
someone could try reproducing the R build error I get with that GCC
version (and '-O3' in CFLAGS et al.).


-leif

[1] http://trac.sagemath.org/sage_trac/ticket/12741

[2] http://trac.sagemath.org/sage_trac/ticket/13150

[leif]

leif@boxen:/home/release$ diff -qr sage-5.1/sage-5.1
sage-5.2.rc1/sage-5.2.rc1 | grep differ | grep '\.spkg'
leif@boxen:/home/release$

Thanks!

(Some newly merged "identical" spkgs in beta0 vs. rc1 and rc0 vs. rc1 of
course still differ at the moment.)