SAGE-2.8.13 released!

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William Stein

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Nov 21, 2007, 6:46:08 PM11/21/07
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Hello folks,

Sage 2.8.13 has been released. Sources are and binaries should soon be
available at

http://sagemath.org/download.html

This is the first release after the excellent Sage Days 6 in Bristol.
We are a couple days late, mostly due to a rocky initial alpha0 that
took some time to sort out and also the new policy that all patches
have to be reviewed before they can get merged.

The usual suspects contributed major pieces to this release:

- Bill Hart
- John Cremona
- Josh Kantor
- Martin Albrecht
- Michael Abshoff
- Mike Hansen
- Ondrej Certik
- Ralf-Philip Weinmann
- Robert Bradshaw
- William Stein
- Willem Jan Palenstijn

Sorry if I forgot anybody, it has been quite a turbulent release
cycle. Thanks to all the reviewers, all the testers, especially
Jaap Spies, and please send me patches for the doctest failures.

Cheers,

Michael Abshoff (release chair), William Stein

* Major Features, New Spkgs and Bugfixes

Major new features are John Cremona's g0n, updates to flint, scipy &
numpy, cvxopt and sympy as well as major bug fixes to libfplll and
memory leak fixes in linbox. This is also the first release that
compiles on OSX 10.5 "out of the box", i.e. without the need to have
gfortran installed.

Updates spkgs in detail:

#563: linbox-20070915.p2.spkg (Michael Abshoff)
#1029: flint-0.9-r1072.spkg (Robert Bradshaw, Michael Abshoff)
#1188: libfplll-2.1.3-20071117.spkg (Martin Albrecht, Michael Abshoff,
Willem Jan Palenstijn, also #1126)
#1177: mpfr-2.3.0.p0.spkg (Michael Abshoff)
#1189: sympy-0.5.7.spkg (Ondrej Certik)
#1197: cremona-20071116.p0.spkg (John Cremona, William Stein,
Ralf-Philip Weinmann)
#1198: scipy-20071020-0.6.spkg (Josh Kantor)
#1198: numpy-20071020-1.0.3.1.spkg (Josh Kantor)
#1199: cvxopt-0.9.p1.spkg (Josh Kantor, Michael Abshoff, also #1121, #1161)

We closed a total of 49 tickets, see

http://www.sagetrac.org/sage_trac/query?status=closed&milestone=sage-2.8.13

for details.

* Known Issues with 2.8.13

- cvxopt fails to import on OSX PPC (ticket #1222)
- g0n, i.e. cremona.spkg fails to compile on Linux/Itanium with
older gcc and also Solaris.

* Upcoming Releases

2.8.14 is planned for next week, depending on how close the release
will be to Sage Bug Day 6 on November 2nd, 2007 we might do another
2.8.15 release the day before. Major spkg candidates for 2.8.14 are

- Singular 3-0-4
- PolyBoRi
- ATLAS BLAS/Lapack

It looks unlikely that we will achieve the major goals for 2.9, namely
Solaris 32 bit support and OSX 10.5 64 bit support, in the next two
weeks, so we might do a couple more 2.8.x releases.

* Coverage

2.8.13:

Overall weighted coverage score: 34.4%
Total number of functions: 17472

Compared to 2.8.12:

Overall weighted coverage score: 34.3%
Total number of functions: 17418

* About Sage (http://www.sagemath.org)

Sage is developed by volunteers and combines 71 open source packages.
It is available for free 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

Jaap Spies

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Nov 21, 2007, 7:04:13 PM11/21/07
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William Stein wrote:
> Hello folks,

>
> 2.8.14 is planned for next week, depending on how close the release
> will be to Sage Bug Day 6 on November 2nd, 2007 we might do another

December 2nd?

Jaap

William Stein

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Nov 21, 2007, 7:05:22 PM11/21/07
to sage-s...@googlegroups.com

Is there something wrong with you time machine yacht?


(yes, dec 2. Thanks.)

-- William

Jaap Spies

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Nov 21, 2007, 7:09:05 PM11/21/07
to sage-s...@googlegroups.com

No, heading to the stars :)!

>
> (yes, dec 2. Thanks.)
>
>

Simon King

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Nov 22, 2007, 5:01:44 AM11/22/07
to sage-s...@googlegroups.com
Dear William,

i met two problems when i upgraded to 2.8.13
(sudo sage -upgrade)

1) The upgrade was interactive. At some point, vim opened, and apparently
i was supposed to insert some text. Is there some "hg commit" involved
in the upgrading process?

2) sage: An error occurred while installing cremona-20071116.p0

You mention that there is an issue with cremona.spkg on Linux/Itanium with
older gcc and also Solaris. My settings are:
- openSUSE 10.2 (X86-64),
- AMD Athlon(tm) 64 Processor 3700+
- gcc-Version 4.2.1; I think this isn't exactly old, or is it?

The gzipped log-file is attached.

Yours sincerely
Simon

install.log.gz

mabshoff

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Nov 22, 2007, 5:25:37 AM11/22/07
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On Nov 22, 11:01 am, Simon King <k...@mathematik.uni-jena.de> wrote:
> Dear William,

Hello Simon,

>
> i met two problems when i upgraded to 2.8.13
> (sudo sage -upgrade)
>
> 1) The upgrade was interactive. At some point, vim opened, and apparently
> i was supposed to insert some text. Is there some "hg commit" involved
> in the upgrading process?

This is because you have local changes. Before 2.8.11 or so when you
upgraded instead of merging the repo it was overwritten.

>
> 2) sage: An error occurred while installing cremona-20071116.p0
>
> You mention that there is an issue with cremona.spkg on Linux/Itanium with
> older gcc and also Solaris. My settings are:
> - openSUSE 10.2 (X86-64),
> - AMD Athlon(tm) 64 Processor 3700+
> - gcc-Version 4.2.1; I think this isn't exactly old, or is it?
>

The system compiler on OpenSuSE 10.2 is rather broken, but you seem to
use gcc 4.2.1, which works perfectly fine on sage.math. I will have a
look at the logs later and see if I can come up with the problem.

> The gzipped log-file is attached.
>

It would be better if you put log files up on the web somewhere and
posted a link. That way 100+ people do not end up with a 1.4MB
attachment in their inbox ;)

> Yours sincerely
> Simon
>

Cheers,

Michael

> install.log.gz
> 1434KDownload

Simon King

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Nov 22, 2007, 8:15:15 AM11/22/07
to sage-support
Dear Michael,

On Nov 22, 11:25 am, mabshoff <Michael.Absh...@fsmath.mathematik.uni-
dortmund.de> wrote:
> > 1) The upgrade was interactive. At some point, vim opened, and apparently
> > i was supposed to insert some text. Is there some "hg commit" involved
> > in the upgrading process?
>
> This is because you have local changes. Before 2.8.11 or so when you
> upgraded instead of merging the repo it was overwritten.

Good idea!
I remember that after previous upgrades, i had to redo changes in sage-
env.

> The system compiler on OpenSuSE 10.2 is rather broken, but you seem to
> use gcc 4.2.1, which works perfectly fine on sage.math. I will have a
> look at the logs later and see if I can come up with the problem.

I succeeded to upgrade on a different machine:
- Again openSUSE 10.2 (X86-64),
- four Dual Core AMD Opteron(tm) Processors 270
- gcc (GCC) 4.1.2 20061115 (prerelease) (SUSE Linux)

So, gcc 4.1.2 did the job, but 4.2.1 didn't.

> It would be better if you put log files up on the web somewhere and
> posted a link. That way 100+ people do not end up with a 1.4MB
> attachment in their inbox ;)

Ok, i hope i will remember it.

Best regards
Simon

Alexander Dreyer

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Nov 23, 2007, 3:15:44 AM11/23/07
to sage-support
sage-2.8.13 fails to build on the following system:
Linux node179 2.6.16.27-0.6-smp-perfctr #2 SMP Thu Oct 11 10:04:48
CEST 2007 x86_64 x86_64 x86_64 GNU/Linux

Best regards,
Alexander Dreyer

PS: The crucial part of the logs:
****************************************************
GCC Version
gcc -v
Es werden eingebaute Spezifikationen verwendet.
Ziel: x86_64-suse-linux
Konfiguriert mit: ../configure --enable-threads=posix --prefix=/usr --
with-local-prefix=/usr/local --infodir=/usr/share/info --mandir=/usr/
share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-
languages=c,c++,objc,fortran,obj-c++,java,ada --enable-
checking=release --with-gxx-include-dir=/usr/include/c++/4.1.2 --
enable-ssp --disable-libssp --disable-libgcj --with-slibdir=/lib64 --
with-system-zlib --enable-shared --enable-__cxa_atexit --enable-
libstdcxx-allocator=new --program-suffix= --enable-version-specific-
runtime-libs --without-system-libunwind --with-cpu=generic --
host=x86_64-suse-linux
Thread-Modell: posix
gcc-Version 4.1.2 20070115 (prerelease) (SUSE Linux)
****************************************************
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/u/herc/dreyer/tmp/sage-2.8.13/spkg/build/mpfi-1.3.4-rc3.p9/src/
missing: Unknown `--run' option
Try `/u/herc/dreyer/tmp/sage-2.8.13/spkg/build/mpfi-1.3.4-rc3.p9/src/
missing --help' for more information
configure: WARNING: `missing' script is too old or missing
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking for gmp.h... yes
checking for valid GMP... yes
checking for mpfr.h... yes
checking for main in -lmpfr... yes
checking for main in -lgmp... no
configure: error: Library GMP not found
Error configuring mpfi

real 0m2.685s
user 0m0.608s
sys 0m0.792s
sage: An error occurred while installing mpfi-1.3.4-rc3.p9


mabshoff

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Nov 23, 2007, 7:38:23 AM11/23/07
to sage-support


On Nov 23, 9:15 am, Alexander Dreyer
<jan.alexander.dre...@googlemail.com> wrote:

Hello Alexander,

> sage-2.8.13 fails to build on the following system:
> Linux node179 2.6.16.27-0.6-smp-perfctr #2 SMP Thu Oct 11 10:04:48
> CEST 2007 x86_64 x86_64 x86_64 GNU/Linux

This looks like a 64 bit SuSE 10.1 box - am I correct?
I have never seen such a failure before and we haven't touched mpfi
for a couple releases. I need to have a closer look at mpfi's
configure system and debug this.

This is now ticket #1246 - see http://www.sagetrac.org/sage_trac/ticket/1246
>
> real 0m2.685s
> user 0m0.608s
> sys 0m0.792s
> sage: An error occurred while installing mpfi-1.3.4-rc3.p9

Cheers,

Michael

William Stein

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Nov 23, 2007, 12:55:21 PM11/23/07
to sage-s...@googlegroups.com
On Nov 23, 2007 4:38 AM, mabshoff

<Michael...@fsmath.mathematik.uni-dortmund.de> wrote:
>
>
>
> On Nov 23, 9:15 am, Alexander Dreyer
> <jan.alexander.dre...@googlemail.com> wrote:
>
> Hello Alexander,
>
> > sage-2.8.13 fails to build on the following system:
> > Linux node179 2.6.16.27-0.6-smp-perfctr #2 SMP Thu Oct 11 10:04:48
> > CEST 2007 x86_64 x86_64 x86_64 GNU/Linux
>
> This looks like a 64 bit SuSE 10.1 box - am I correct?

Also, do you have GMP installed system-wide? It could be
some broken weird GMP that confuses the mpfi build
script.

It could also be some very weird error in sage the build system
itself, where maybe it somehow tries to build mpfi but gmp didn't
get installed correctly -- could you post your install.log online somewhere
and email us a link to it?

--

mabshoff

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Nov 23, 2007, 2:58:09 PM11/23/07
to sage-support


On Nov 23, 6:55 pm, "William Stein" <wst...@gmail.com> wrote:
> On Nov 23, 2007 4:38 AM, mabshoff
>
> <Michael.Absh...@fsmath.mathematik.uni-dortmund.de> wrote:
>
> > On Nov 23, 9:15 am, Alexander Dreyer
> > <jan.alexander.dre...@googlemail.com> wrote:
>

Hello Alexander,

> > Hello Alexander,
>
> > > sage-2.8.13 fails to build on the following system:
> > > Linux node179 2.6.16.27-0.6-smp-perfctr #2 SMP Thu Oct 11 10:04:48
> > > CEST 2007 x86_64 x86_64 x86_64 GNU/Linux
>
> > This looks like a 64 bit SuSE 10.1 box - am I correct?
>
> Also, do you have GMP installed system-wide? It could be
> some broken weird GMP that confuses the mpfi build
> script.

Yep, I suspect something similar, but I have a couple more questions:

> It could also be some very weird error in sage the build system
> itself, where maybe it somehow tries to build mpfi but gmp didn't
> get installed correctly -- could you post your install.log online somewhere
> and email us a link to it?
>

1) Is this a virgin build or an upgrade?

2) If an upgrade: What version did you upgrade from? Was that a binary
or also build from source?

3) Have previous versions build successfully on that particular box?
If so which ones?

gzipping the install.log and putting it up somewhere for us to
download would probably help a great bit.

Cheers,

Michael
> > This is now ticket #1246 - seehttp://www.sagetrac.org/sage_trac/ticket/1246

Alexander Dreyer

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Nov 24, 2007, 11:11:03 AM11/24/07
to sage-support
Hello William and Michael,

> > > This looks like a 64 bit SuSE 10.1 box - am I correct?
Yes.
> > Also, do you have GMP installed system-wide? It could be
> > some broken weird GMP that confuses the mpfi build
> > script.
Yes, GMP ist installed systemwide.

> Yep, I suspect something similar, but I have a couple more questions:
>
> > It could also be some very weird error in sage the build system
> > itself, where maybe it somehow tries to build mpfi but gmp didn't
> > get installed correctly -- could you post your install.log online somewhere
> > and email us a link to it?
>
> 1) Is this a virgin build or an upgrade?
This is a complete virgin build.
> 2) If an upgrade: What version did you upgrade from? Was that a binary
> or also build from source?
>
> 3) Have previous versions build successfully on that particular box?
> If so which ones?
I realized that 2.8.12 also do not compile. (Your servers were renewed
recently, so this was a first attempt to build sage on it.)
Meanwhile, I got sage compiled by changing the configure line in spkg-
install of mpfi-1.3.4-rc3.p9 to
./configure --prefix="$SAGE_LOCAL" --with-mpfr-dir="$SAGE_LOCAL"
CFLAGS="-fPIC"

> gzipping the install.log and putting it up somewhere for us to
> download would probably help a great bit.
See here:
http://polybori.sourceforge.net/tmp/installlog_sage.tar.bz2

Best regards,
Alexander Dreyer

mabshoff

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Nov 24, 2007, 11:16:36 AM11/24/07
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On Nov 24, 5:11 pm, Alexander Dreyer
<jan.alexander.dre...@googlemail.com> wrote:
> Hello William and Michael,
>
> > > > This looks like a 64 bit SuSE 10.1 box - am I correct?
> Yes.
> > > Also, do you have GMP installed system-wide? It could be
> > > some broken weird GMP that confuses the mpfi build
> > > script.
>
> Yes, GMP ist installed systemwide.
>
> > Yep, I suspect something similar, but I have a couple more questions:
>
> > > It could also be some very weird error in sage the build system
> > > itself, where maybe it somehow tries to build mpfi but gmp didn't
> > > get installed correctly -- could you post your install.log online somewhere
> > > and email us a link to it?
>
> > 1) Is this a virgin build or an upgrade?
>
> This is a complete virgin build.> 2) If an upgrade: What version did you upgrade from? Was that a binary
> > or also build from source?
>
> > 3) Have previous versions build successfully on that particular box?
> > If so which ones?
>

Hello Alexander,

> I realized that 2.8.12 also do not compile. (Your servers were renewed
> recently, so this was a first attempt to build sage on it.)
> Meanwhile, I got sage compiled by changing the configure line in spkg-
> install of mpfi-1.3.4-rc3.p9 to
> ./configure --prefix="$SAGE_LOCAL" --with-mpfr-dir="$SAGE_LOCAL"
> CFLAGS="-fPIC"
>

Ok, if that does the trick I will merge the fix into 2.8.14 provided
it compiles locally on the test boxen (which it should). I looked at
the configure log in detail and it seems very weired that it fails
that late because it does find a gmp and gmp headers.

Oh well, Sage never builds out of the box for everybody. It is like
playing a whack a mole :)

Michael

Alexander Dreyer

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Nov 25, 2007, 5:51:27 AM11/25/07
to sage-support
Hello Michael,

> Ok, if that does the trick I will merge the fix into 2.8.14 provided
> it compiles locally on the test boxen (which it should). I looked at
> the configure log in detail and it seems very weired that it fails
> that late because it does find a gmp and gmp headers.
Hm, I'm not sure, whether my patch is more a workaround than the
actual solution.
In the original spsk_install it reads '--with-gmp-dir="$SAGE_LOCAL" '.
So gmo is also searched for in SAGE_LOCAL. But there is no libgmp.a in
SAGE_LOCAL (only .so, .la ...). I suspect, it should be there
independent of the case whether there is a system-wide gmp, doesn't
it?

> Oh well, Sage never builds out of the box for everybody. It is like
> playing a whack a mole :)
Indeed, indeed. First I had to change to a different servers, because
it didn't build on "my" machine, because of the usual gcc 4.1.0
compiler-bug. (I'm still waiting for our edp-department to update gcc
on my usual machine.)

Best regards,
Alexander
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