sage-5.0.beta14 released

[Jeroen Demeyer]

Dear Sage lovers,

We're releasing Sage 5.0.beta14.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14/

Currently there is a technical problem with the mirroring, which means
this beta release is only available from the above location.


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

== Tickets ==

* We closed 482 tickets in this release. For details, see

http://boxen.math.washington.edu/home/release/sage-5.0.beta14/tickets.html

Closed tickets:

#11909: Merging fixes for PolyBoRi 0.7.1 into 0.8 spkg [Reviewed by
Alexander Dreyer, Leif Leonhardy]
#12435: lcalc does not respect global CXX flag [Reviewed by Leif Leonhardy]
#12441: singular does not respect global cxx flag [Reviewed by Leif
Leonhardy]
#12700: stopgap for #11832 [Reviewed by John Palmieri]
#12710: Stopgap for 11358 [Reviewed by Michael Orlitzky]

Merged in sage-5.0.beta14:

#8577: Martin Albrecht: Fix ETuple.eadd_p [Reviewed by Mike Hansen]
#8720: Jason Grout, Mike Hansen, Paul Zimmermann: CC and CDF do not
display numeric 0 [Reviewed by Paul Zimmermann, Karl-Dieter Crisman]
#9826: Johan Bosman, Michael Orlitzky: Memory corruption in polynomial
complex_roots() method [Reviewed by Michael Orlitzky, Johan Bosman,
Volker Braun]
#10281: William Stein: Multimodular echelon form over cyclotomic fields
fails [Reviewed by Martin Raum]
#10328: Julien Puydt: Flint-1.5.2 with ARM 32-bits [Reviewed by Dmitrii
Pasechnik]
#10901: Alex Ghitza: segfault in roots() in wrong ring [Reviewed by
Michael Orlitzky]
#10914: Michael Orlitzky: Integration involving abs gives wrong result
[Reviewed by Karl-Dieter Crisman]
#11625: John Palmieri: speed up "remove_faces" for simplicial complexes
[Reviewed by Mike Hansen]
#12169: Fidel Barrera-Cruz: Adding Harary graphs to graph generators.
[Reviewed by David Coudert, Nathann Cohen]
#12347: Punarbasu Purkayastha: make install broken in Sage 4.8 [Reviewed
by Jeroen Demeyer, Paul Zimmermann]
#12493: John Palmieri: tol and optional in doctests don't play well
together [Reviewed by Marco Streng]
#12536: Anne Schilling, Nicolas M. Thiéry: Implementation of class for
Linear Extensions of a finite Poset [Reviewed by Nicolas M. Thiéry, Anne
Schilling]
#12551: Julian Rueth: characteristic() does not work for extensions for
function field [Reviewed by Jeroen Demeyer]
#12568: Itai Bar-Natan, Jean-Pierre Flori: make doesn't work properly
for targets 'test' and 'micro_release' [Reviewed by Jeroen Demeyer]
#12596: Benjamin Jones: poor documentation of elliptic integrals in
functions/special.py [Reviewed by Karl-Dieter Crisman, Jeroen Demeyer]
#12597: Mike Hansen: Error in creating a Permutation Group [Reviewed by
Daniel Krenn]
#12620: Karl-Dieter Crisman: problems with bezier3d command [Reviewed by
Michael Orlitzky]
#12636: Johan Bosman: 0.is_squarefree() raises a PariError [Reviewed by
Jeroen Demeyer]
#12717: Florent Hivert: Add \NN to standard latex constant, fixes a few
glitches in LaTeX/HTML output [Reviewed by Nicolas M. Thiéry]
#12766: David Roe: Better plotting for elliptic curves [Reviewed by
Kiran Kedlaya]
#12769: David Roe: Better error message when looking up an elliptic
curve by nonexistent label [Reviewed by Mike Hansen]
#12791: David Coudert: Running time improvements of some (di)graphs
products [Reviewed by Nathann Cohen]
#12796: Nils Bruin: Allow more general evaluation of FDerivativeOperator
[Reviewed by Michael Orlitzky]
#12800: Jeroen Demeyer: Upgrade zlib to 1.2.6 [Reviewed by Michael
Orlitzky, Julien Puydt, Leif Leonhardy]
#12801: Nils Bruin: substitute_function misses some substitutions
[Reviewed by Michael Orlitzky]
#12820: Jeroen Demeyer: OS X Lion: use "clang" as default C compiler
[Reviewed by Leif Leonhardy]
#12825: Jeroen Demeyer: Fine-tune auto-detection of whether to install
GCC [Reviewed by Dan Drake, Leif Leonhardy]
#12829: Paul Zimmermann, Jeroen Demeyer: Remove <object> cast in
real_mpfi.pyx [Reviewed by François Bissey]
#12849: Florent Hivert, Jeroen Demeyer: The argspecs of extension
function/methods is broken in the Sphinx documentation [Reviewed by Mike
Hansen]
#12853: Andrey Novoseltsev: Severe slow-down in elliptic_curve
integral_points() [Reviewed by Jeroen Demeyer]

[Dan Drake]

On Fri, 27 Apr 2012 at 08:34AM +0200, Jeroen Demeyer wrote:
> Currently there is a technical problem with the mirroring, which means
> this beta release is only available from the above location.

...and also at http://sagenb.kaist.ac.kr/~drake/sage-5.0.beta14.tar, in
case someone's connection to Korea is faster than their connection to
Seattle...

Dan

--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------

[Anthony David]

My woes with building 5.0 beta xx on Ubuntu i386 continue. I upgraded the server to Oneiric and after this kluge to get it to use the pre-built atlas libs:

ln -s /usr/lib/atlas-base/atlas/liblapack.a /usr/lib/atlas-base/liblapack.a

-

...

/home/adavid/build/sage-5.0.beta14/spkg/pipestatus "sage-spkg ${SAGE_SPKG_OPTS} matplotlib-1.1.0 2>&1" "tee -a /home/adavid/build/sage-5.0.beta14/spkg/logs/matplotlib-1.1.0.log"

matplotlib-1.1.0

====================================================

Extracting package /home/adavid/build/sage-5.0.beta14/spkg/standard/matplotlib-1.1.0.spkg

-rw-r--r-- 1 adavid adavid 8607075 2012-04-26 18:18 /home/adavid/build/sage-5.0.beta14/spkg/standard/matplotlib-1.1.0.spkg

Finished extraction

****************************************************

Host system:

Linux test.fishreading.com 3.0.0-17-generic-pae #30-Ubuntu SMP Thu Mar 8 17:53:35 UTC 2012 i686 i686 i386 GNU/Linux

****************************************************

C compiler: gcc

C compiler version:

Using built-in specs.

COLLECT_GCC=gcc

COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6.1/lto-wrapper

Target: i686-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.1-9ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++,go --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-plugin --enable-objc-gc --enable-targets=all --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu

Thread model: posix

gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3) 

****************************************************

NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the Matplotlib GUI.

Not building any matplotlib graphical backends.

patching file lib/matplotlib/__init__.py

patching file lib/matplotlib/finance.py

patching file lib/matplotlib/texmanager.py

patching file setupext.py

basedirlist is: ['/home/adavid/build/sage-5.0.beta14/local']

============================================================================

BUILDING MATPLOTLIB

            matplotlib: 1.1.0

                python: 2.7.2 (default, Apr 27 2012, 07:07:28)  [GCC 4.6.1]

              platform: linux3

REQUIRED DEPENDENCIES

                 numpy: no

                        * You must install numpy 1.1 or later to build

                        * matplotlib.

Error building matplotlib package.

real    0m0.311s

user    0m0.212s

sys     0m0.068s

************************************************************************

Error installing package matplotlib-1.1.0

************************************************************************

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file

  /home/adavid/build/sage-5.0.beta14/spkg/logs/matplotlib-1.1.0.log

Describe your computer, operating system, etc.

If you want to try to fix the problem yourself, *don't* just cd to

/home/adavid/build/sage-5.0.beta14/spkg/build/matplotlib-1.1.0 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 '/home/adavid/build/sage-5.0.beta14/spkg/build/matplotlib-1.1.0' && '/home/adavid/build/sage-5.0.beta14/sage' -sh)

When you are done debugging, you can type "exit" to leave the subshell.

************************************************************************

make[1]: *** [installed/matplotlib-1.1.0] Error 1

make[1]: Leaving directory `/home/adavid/build/sage-5.0.beta14/spkg'

real    59m15.555s

user    41m7.614s

sys     8m7.074s

Error building Sage.

make: *** [build] Error 1

Note: numpy reported to be installed earlier in the install log:

real    2m35.841s

user    2m19.605s

sys     0m9.073s

Successfully installed numpy-1.5.1.p1

Package numpy-1.5.1.p1 has no test suite.

Deleting temporary build directory

/home/adavid/build/sage-5.0.beta14/spkg/build/numpy-1.5.1.p1

Making Python scripts relocatable...

Finished installing numpy-1.5.1.p1.spkg

Regards

Anthony David

Full install.log from ftp://adavid.com.au/install.log.gz

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[leif]

Anthony David wrote:
> My woes with building 5.0 beta xx on Ubuntu i386 continue. I upgraded
> the server to Oneiric and after this kluge to get it to use the
> pre-built atlas libs:
>
> ln -s /usr/lib/atlas-base/atlas/liblapack.a /usr/lib/atlas-base/liblapack.a
>
> -
> ...
>
> /home/adavid/build/sage-5.0.beta14/spkg/pipestatus "sage-spkg
> ${SAGE_SPKG_OPTS} matplotlib-1.1.0 2>&1" "tee -a
> /home/adavid/build/sage-5.0.beta14/spkg/logs/matplotlib-1.1.0.log"
> matplotlib-1.1.0
> ====================================================
> Extracting package
> /home/adavid/build/sage-5.0.beta14/spkg/standard/matplotlib-1.1.0.spkg
> -rw-r--r-- 1 adavid adavid 8607075 2012-04-26 18:18
> /home/adavid/build/sage-5.0.beta14/spkg/standard/matplotlib-1.1.0.spkg
> Finished extraction
> ****************************************************
> Host system:

> Linux test.fishreading.com <http://test.fishreading.com>

def check_for_numpy():
try:
import numpy
except ImportError:
print_status("numpy", "no")
print_message("You must install numpy 1.1 or later to build
matplotlib.")
return False
nn = numpy.__version__.split('.')
if not (int(nn[0]) >= 1 and int(nn[1]) >= 1):
if not (int(nn[0]) >= 2):
print_message(
'numpy 1.1 or later is required; you have %s' %
numpy.__version__)
return False
module = Extension('test', [])
add_numpy_flags(module)
add_base_flags(module)

print_status("numpy", numpy.__version__)
if not find_include_file(module.include_dirs, os.path.join("numpy",
"arrayobject.h")):
print_message("Could not find the headers for numpy. You may
need to install the development package.")
return False
return True


So you should try what

$ ./sage --python 'import numpy'

gives.


-leif

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

[Anthony David]

Type "help", "copyright", "credits" or "license" for more information.

>>> import numpy

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/home/adavid/build/sage-5.0.beta14/local/lib/python2.7/site-packages/numpy/__init__.py", line 136, in <module>

    import add_newdocs

  File "/home/adavid/build/sage-5.0.beta14/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>

    from numpy.lib import add_newdoc

  File "/home/adavid/build/sage-5.0.beta14/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module>

    from polynomial import *

  File "/home/adavid/build/sage-5.0.beta14/local/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 17, in <module>

    from numpy.linalg import eigvals, lstsq

  File "/home/adavid/build/sage-5.0.beta14/local/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 48, in <module>

    from linalg import *

  File "/home/adavid/build/sage-5.0.beta14/local/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 23, in <module>

    from numpy.linalg import lapack_lite

ImportError: libatlas.so.3gf: cannot open shared object file: No such file or directory

>>>  

And

adavid@test:~/build/sage-5.0.beta14/local/lib/python2.7/site-packages/numpy/linalg$ ldd lapack_lite.so 

        linux-gate.so.1 =>  (0x00bca000)

        libatlas.so.3gf => not found

        libpython2.7.so.1.0 => /usr/lib/libpython2.7.so.1.0 (0x00110000)

        libgfortran.so.3 => /usr/lib/i386-linux-gnu/libgfortran.so.3 (0x006b6000)

        libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0x00a34000)

        libgcc_s.so.1 => /lib/i386-linux-gnu/libgcc_s.so.1 (0x00586000)

        libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0x007b8000)

        libssl.so.1.0.0 => /lib/i386-linux-gnu/libssl.so.1.0.0 (0x003d4000)

        libcrypto.so.1.0.0 => /lib/i386-linux-gnu/libcrypto.so.1.0.0 (0x00bcb000)

        libz.so.1 => /lib/i386-linux-gnu/libz.so.1 (0x00421000)

        libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0x00436000)

        libdl.so.2 => /lib/i386-linux-gnu/libdl.so.2 (0x00451000)

        libutil.so.1 => /lib/i386-linux-gnu/libutil.so.1 (0x00dcf000)

        libquadmath.so.0 => /usr/lib/i386-linux-gnu/libquadmath.so.0 (0x004b0000)

        /lib/ld-linux.so.2 (0x00490000)

 Note:

Built with

export SAGE_ATLAS_LIB=/usr/lib/atlas-base

export SAGE_CHECK="yes"

Fixed with

adavid@test:~/build/sage-5.0.beta14$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/atlas-base

adavid@test:~/build/sage-5.0.beta14$ ./sage -python

Python 2.7.2 (default, Apr 27 2012, 07:07:28) 

[GCC 4.6.1] on linux3

Type "help", "copyright", "credits" or "license" for more information.

>>> import numpy

Looks like a bit of experimenting with update-alternatives is in order

[Anthony David]

On Fri, Apr 27, 2012 at 4:34 PM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:

Dear Sage lovers,

We're releasing Sage 5.0.beta14.

************************************************************************

Error testing package libm4rie-20111004.p2

************************************************************************

Tests reported FAIL'ed  in exact same fashion as reported for sage-5.0.beta12

 

http://groups.google.com/group/sage-release/browse_thread/thread/a6e8d8597cabe127

Haven't found what is incrementing the error counter to throw the FAIL messages despite

the tests reporting 'success'

Regards

Anthony

[Franco Saliola]

On Fri, Apr 27, 2012 at 2:34 AM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.0.beta14.

$ uname -a
Darwin lacim-macpro-02 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7
16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64

$ make
...
Sage build/upgrade complete!

$ make ptest
...
----------------------------------------------------------------------

The following tests failed:

sage -t -force_lib devel/sage/sage/interacts/debugger.py # 9
doctests failed
sage -t -force_lib devel/sage/sage/interfaces/sage0.py # 30
doctests failed
sage -t -force_lib devel/sage/sage/misc/randstate.pyx # 3
doctests failed
sage -t -force_lib devel/sage/sage/tests/startup.py # 1 doctests failed
----------------------------------------------------------------------
Total time for all tests: 656.2 seconds

See attached file for details of the failures.

Take care,
Franco

--

[Justin C. Walker]

On Apr 26, 2012, at 23:34 , Jeroen Demeyer wrote:

> Dear Sage lovers,
>
> We're releasing Sage 5.0.beta14.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14.tar

Two builds to report:

Built from scratch on Mac OS X, 10.6.8 (Dual 6-core Xeons). No problems with build, docs, or testing ('ptestlong')!

Built from scratch on Mac OS X, 10.7.1 (4-core Core i7): two packages had build failures:
MPIR (mpir-2.1.3.p9.spkg)
ECM (ecm-6.3.p4.spkg)
Logs available if needed.

I replaced these with newer .spkg's from trac:
mpir-2.4.0.p2.spkg (#11616)
ecm-6.3.p7.spkg (#12830)
The build, doc build, and testing ('ptestlong') then completed with no problems!

I have not built "from scratch" with the new .spkg's; that is underway now, but I expect no problems, given the above.

Justin

--
Justin C. Walker, Curmudgeon at Large
Director
Institute for the Enhancement of the Director's income
-----------
Question 43:
What if the hokey pokey
really *is* what it’s all about?
--

[Dr. David Kirkby]

On 04/27/12 07:34 AM, Jeroen Demeyer wrote:
> Dear Sage lovers,
>
> We're releasing Sage 5.0.beta14.
>
> Source archive:
>
> http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14.tar

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

OK, here's a set of results from a computer I've never used before. It is NOT
the computer I said I'd build Sage on, as it is busy doing higher priority
tasks. I got two test failures, but they both passed on a second run.

Has the issue with testing in parallel not be solved?



* IBM x3550 server
* 1 x Intel(R) Xeon(R) CPU quad-core E5430 @ 2.66GHz, 6 MB cache
* 32 GB RAM

The OS is CentOS release 4.7 (Final). This is binary compatible with Red Hat
Enterprise Linux AS release 4 (Nahant Update 7).



The following tests failed:

sage -t --long -force_lib devel/sage/doc/en/constructions/plotting.rst # 2
doctests failed
sage -t --long -force_lib devel/sage/sage/combinat/combinat.py # 2 doctests failed
----------------------------------------------------------------------
Total time for all tests: 2000.1 seconds
make: *** [ptestlong] Error 128
[drkirkby@skylark sage-5.0.beta14]$
[drkirkby@skylark sage-5.0.beta14]$
[drkirkby@skylark sage-5.0.beta14]$ ./sage -t --long -force_lib
devel/sage/sage/combinat/combinat.py
sage -t --long -force_lib "devel/sage/sage/combinat/combinat.py"
[5.1 s]

----------------------------------------------------------------------
All tests passed!
Total time for all tests: 5.2 seconds
[drkirkby@skylark sage-5.0.beta14]$ ./sage -t --long -force_lib
devel/sage/doc/en/constructions/plotting.rst
sage -t --long -force_lib "devel/sage/doc/en/constructions/plotting.rst"
[12.8 s]

----------------------------------------------------------------------
All tests passed!
Total time for all tests: 12.8 seconds
[drkirkby@skylark sage-5.0.beta14]$


Dave

[Jeroen Demeyer]

On 2012-04-28 22:35, Dr. David Kirkby wrote:
> Has the issue with testing in parallel not be solved?

Which issue? There are flaky tests which sometimes randomly fail. I
don't think these only fail when testing in parallel.

[David Kirkby]

I know the method of testing Sage has been less than perfect, but I
believe some of the issues were problematic when testing in parallel,
as two processes could be using the same temporary directory. I know
people were working on that, but I don't know if it ever got finished.

It's worrying if the tests are flaky.

Anyway, it would appear that Sage does build and can pass all tests on
CentOS 4.7, so I assume Redhat 4.7 too. That is an old version of the
OS.

Dave

[oscarvarto]

I'm a Sage lover but cannot build Sage5.0.beta14 on Mac OS X Lion 10.7.3

I get the following error:

no, double -> ulong conversion
configure: error: could not find a working compiler, see config.log for details
sage_fortran -fPIC -c slasd4.f -o slasd4.o
Error configuring MPIR. (See above for the options passed to it.)

real 1m0.721s
user 0m17.308s
sys 0m20.156s
************************************************************************
Error installing package mpir-2.1.3.p9
************************************************************************

Under spkg/build/mpir-2.1.3.p9/src I have config.log, which I pasted here:
http://pastebin.com/zKBwLHgK

The relevant part is at lines 119-126 (I believe):
failed program was:
/* The following provokes a linker invocation problem with gcc 3.0.3
on AIX 4.3 under "-maix64 -mpowerpc64 -mcpu=630". The -mcpu=630
option causes gcc to incorrectly select the 32-bit libgcc.a, not
the 64-bit one, and consequently it misses out on the __fixunsdfdi
helper (double -> uint64 conversion). */
double d;
unsigned long gcc303 () { return (unsigned long) d; }

I don't know how to correct this by myself, Please help!

I have done this
$ sudo mv /opt/local /opt/localT
so that the installation can't see MacPorts installation.
Have everything updated, XCode, etc.

Haven't test it on Arch Linux (generally easier)

[leif]

Justin C. Walker wrote:
>
> On Apr 26, 2012, at 23:34 , Jeroen Demeyer wrote:
>
>> Dear Sage lovers,
>>
>> We're releasing Sage 5.0.beta14.
>>
>> Source archive:
>>
>> http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14.tar
>
> Two builds to report:
>
> Built from scratch on Mac OS X, 10.6.8 (Dual 6-core Xeons). No problems with build, docs, or testing ('ptestlong')!
>
> Built from scratch on Mac OS X, 10.7.1 (4-core Core i7): two packages had build failures:
> MPIR (mpir-2.1.3.p9.spkg)
> ECM (ecm-6.3.p4.spkg)
> Logs available if needed.
>
> I replaced these with newer .spkg's from trac:
> mpir-2.4.0.p2.spkg (#11616)

Is that a typo or did you actually use (one of) the old p2(s)? (There's
a p3 since a while.)


-leif

> ecm-6.3.p7.spkg (#12830)
> The build, doc build, and testing ('ptestlong') then completed with no problems!
>
> I have not built "from scratch" with the new .spkg's; that is underway now, but I expect no problems, given the above.
>
> Justin
>
> --
> Justin C. Walker, Curmudgeon at Large
> Director
> Institute for the Enhancement of the Director's income
> -----------
> Question 43:
> What if the hokey pokey

> really *is* what it�s all about?
> --

[leif]

oscarvarto wrote:
> I'm a Sage lover but cannot build Sage5.0.beta14 on Mac OS X Lion 10.7.3
>
> I get the following error:
>
> no, double -> ulong conversion
> configure: error: could not find a working compiler, see config.log for details
> sage_fortran -fPIC -c slasd4.f -o slasd4.o
> Error configuring MPIR. (See above for the options passed to it.)
>
> real 1m0.721s
> user 0m17.308s
> sys 0m20.156s
> ************************************************************************
> Error installing package mpir-2.1.3.p9
> ************************************************************************

On MacOS X 10.7 with more recent CPUs, you have to use the MPIR
2.4.0[.p3] spkg from #11616 [1] (cf. Justin's post).

> Under spkg/build/mpir-2.1.3.p9/src I have config.log, which I pasted here:
> http://pastebin.com/zKBwLHgK
>
> The relevant part is at lines 119-126 (I believe):
> failed program was:
> /* The following provokes a linker invocation problem with gcc 3.0.3
> on AIX 4.3 under "-maix64 -mpowerpc64 -mcpu=630". The -mcpu=630
> option causes gcc to incorrectly select the 32-bit libgcc.a, not
> the 64-bit one, and consequently it misses out on the __fixunsdfdi
> helper (double -> uint64 conversion). */
> double d;
> unsigned long gcc303 () { return (unsigned long) d; }
>
> I don't know how to correct this by myself, Please help!
>
> I have done this
> $ sudo mv /opt/local /opt/localT
> so that the installation can't see MacPorts installation.
> Have everything updated, XCode, etc.
>
> Haven't test it on Arch Linux (generally easier)

The issue above is caused by Apple's assembler, which doesn't know AVX.


Just in case you don't want to use the new MPIR spkg, a work-around with
the old MPIR 2.1.3.p9 spkg is to specify some [more generic] arch/CPU in
CFLAGS; you could e.g. do

$ export CFLAGS="-march=corei7 -mno-avx -O3 -fno-strict-aliasing"
$ make

OR, better,

$ env CFLAGS="-march=corei7 -mno-avx -O3" ./sage -i
spkg/standard/mpir-2.1.3.p9.spkg
$ make


-leif

[Jeroen Demeyer]

On 2012-04-29 03:02, oscarvarto wrote:
> I'm a Sage lover but cannot build Sage5.0.beta14 on Mac OS X Lion 10.7.3

This is a known problem, it should be fixed in the next beta release.

[Justin C. Walker]

On Apr 29, 2012, at 04:28 , leif wrote:

> Justin C. Walker wrote:
>>
>> On Apr 26, 2012, at 23:34 , Jeroen Demeyer wrote:
>>
>>> Dear Sage lovers,
>>>
>>> We're releasing Sage 5.0.beta14.
>>>
>>> Source archive:
>>>
>>> http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14.tar
>>
>> Two builds to report:
>>
>> Built from scratch on Mac OS X, 10.6.8 (Dual 6-core Xeons). No problems with build, docs, or testing ('ptestlong')!
>>
>> Built from scratch on Mac OS X, 10.7.1 (4-core Core i7): two packages had build failures:
>> MPIR (mpir-2.1.3.p9.spkg)
>> ECM (ecm-6.3.p4.spkg)
>> Logs available if needed.
>>
>> I replaced these with newer .spkg's from trac:
>> mpir-2.4.0.p2.spkg (#11616)
>
> Is that a typo or did you actually use (one of) the old p2(s)? (There's a p3 since a while.)

That seems to be a typo, but my recollection is that I copy/pasted that, rather than typed it in by hand. The .spkg that was actually built is "mpir-2.4.0.p3.spkg".

Thanks for catching that.

Justin

--
Justin C. Walker, Curmudgeon at Large

Institute for the Absorption of Federal Funds
-----------
Like the ski resort full of girls hunting for husbands
and husbands hunting for girls, the situation is not
as symmetrical as it might seem.
- Alan MacKay
--

[Benjamin Jones]

I'm getting the "ImportError: No module named crypt" error when building 5.0.beta14. I've built almost all the previous 5.0.betaX releases without any problem on the same machine, so I'm confused. There was a software update applied recently, so that might be the cause. What packages might have been updated that would cause this?

This is a debian/testing x86_64 machine:

jonesbe@sage:/etc$ cat debian_version
6.0.4

jonesbe@sage:/etc$ uname -a
Linux sage 2.6.32 #1 SMP Fri Sep 2 21:08:57 CDT 2011 x86_64 GNU/Linux

--
Benjamin Jones

[Jeroen Demeyer]

On 2012-04-30 06:27, Benjamin Jones wrote:
> I'm getting the "ImportError: No module named crypt" error when building
> 5.0.beta14.

Can you post the Python build log?

And also the output of
$ gcc -v -x c /dev/null -c -o /dev/null

[Anthony David]

On Fri, Apr 27, 2012 at 4:34 PM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:

Dear Sage lovers,

We're releasing Sage 5.0.beta14.

Source archive:

http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14.tar

Upgrade path:

http://boxen.math.washington.edu/home/release/sage-5.0.beta14/sage-5.0.beta14/

Currently there is a technical problem with the mirroring, which means
this beta release is only available from the above location.


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

Fedora 16 x86_64 Built OK after initial nit:

Did not set SAGE_ATLAS_LIB 

Initial Sagetex build failure.

NB: I'm  using texlive 2011 repo

Fixed with yum install texlive-makecmds

install.log extract:

...

! LaTeX Error: File `makecmds.sty' not found.

Type X to quit or <RETURN> to proceed,

or enter new name. (Default extension: sty)

Enter file name: 

! Emergency stop.

<read *> 

         

l.78 \RequirePackage

                    {ifpdf}^^M

No pages of output.

Transcript written on example.log.

Error typesetting example.tex!

[Benjamin Jones]

> --
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>

Hi Jeroen,

I've posted the python log here:
http://sage.math.washington.edu/home/bjones/python-2.7.2.p4.log

and this is the output you asked for:

jonesbe@sage$ gcc -v -x c /dev/null -c -o /dev/null
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian
4.4.7-1' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.4 --enable-shared --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext
--enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
--libdir=/usr/lib --enable-nls --enable-clocale=gnu
--enable-libstdcxx-debug --enable-objc-gc --with-arch-32=i586
--with-tune=generic --enable-checking=release --build=x86_64-linux-gnu
--host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.7 (Debian 4.4.7-1)
COLLECT_GCC_OPTIONS='-v' '-c' '-o' '/dev/null' '-mtune=generic'
/usr/lib/gcc/x86_64-linux-gnu/4.4.7/cc1 -quiet -v -imultilib .
-imultiarch x86_64-linux-gnu /dev/null -quiet -dumpbase null
-mtune=generic -auxbase-strip /dev/null -version -o /tmp/cco5g4IB.s
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory
"/usr/lib/gcc/x86_64-linux-gnu/4.4.7/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
/usr/local/include
/usr/lib/gcc/x86_64-linux-gnu/4.4.7/include
/usr/lib/gcc/x86_64-linux-gnu/4.4.7/include-fixed
/usr/include/x86_64-linux-gnu
/usr/include
End of search list.
GNU C (Debian 4.4.7-1) version 4.4.7 (x86_64-linux-gnu)
compiled by GNU C version 4.4.7, GMP version 5.0.4, MPFR
version 3.1.0-p3.
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: cd973177aab5536e5f28ce4dfbd7f875
COLLECT_GCC_OPTIONS='-v' '-c' '-o' '/dev/null' '-mtune=generic'
as -V -Qy -o /dev/null /tmp/cco5g4IB.s
GNU assembler version 2.20.1 (x86_64-linux-gnu) using BFD version (GNU
Binutils for Debian) 2.20.1-system.20100303
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.4.7/:/usr/lib/gcc/x86_64-linux-gnu/4.4.7/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.4.7/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.4.7/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.4.7/:/usr/lib/gcc/x86_64-linux-gnu/4.4.7/:/usr/lib/gcc/x86_64-linux-gnu/4.4.7/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.4.7/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.4.7/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-c' '-o' '/dev/null' '-mtune=generic'


--
Benjamin Jones
benjami...@gmail.com

[Volker Braun]

Your log says:

*** WARNING: renaming "crypt" since importing it failed: build/lib.linux-x86_64-2.7/crypt.so: undefined symbol: crypt

This symbol should be provided by libcrypt, which is part of glibc.

On Monday, April 30, 2012 10:08:05 AM UTC-4, Benjamin Jones wrote:

On Mon, Apr 30, 2012 at 1:49 AM, Jeroen Demeyer <jdem...@cage.ugent.be> wrote:
> On 2012-04-30 06:27, Benjamin Jones wrote:
>> I'm getting the "ImportError: No module named crypt" error when building
>> 5.0.beta14.
> Can you post the Python build log?
>
> And also the output of
> $ gcc -v -x c /dev/null -c -o /dev/null
>
> --
> 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+unsubscribe@googlegroups.com.

[Jeroen Demeyer]

This is a known problem with recent versions of Debian/Ubuntu. The
following should help:

sudo apt-get install dpkg-dev

[leif]

... which should be printed by our Python spkg as an error message,
shouldn't it?