Upgrade Singular

[jdemeyer]

Upgrade Singular to ​version 3-1-5 (released 12 July 2012).

New spkg: ​http://boxen.math.washington.edu/home/jdemeyer/spkg/singular-3-1-5.p0.spkg

singular-3-1-5.p0 (Jeroen Demeyer, 26 July 2012)

• Trac #13237: Upgrade to version 3-1-5.
• Removed patches which are now upstreamed:
  • patches/Singular.Makefile.in.shared.patch
  • patches/Singular.configure.patch
  • patches/factory.GNUmakefile.in.patch
  • patches/factory_configure
  • patches/make_parallel.patch
  • patches/os_x_ppc.patch
• Put the two patches for SAGE_DEBUG (Singular.Makefile.in.debug.patch and kernel.Makefile.in.debug.patch) into one file sage_debug.patch.
• Add NTL_negate.patch to change negate() to NTL::negate(), see ​http://www.singular.uni-kl.de:8002/trac/ticket/437
• Only unset LD on Darwin.
• Remove the unsetting of TMPDIR (bug fixed upstream).
• Do not override user-set CFLAGS and CXXFLAGS.
• Echo all error message to stderr instead of stdout.
• Fix various ./configure options and remove some unsupported options.
• Always configure --with-debug, as --without-debug doesn't work, see ​http://www.singular.uni-kl.de:8002/trac/ticket/438
• In spkg-install, remove distclean() step; merge clean_headers() and part of the old distclean() into remove_old_version().
• Don't create sage_singular symlink, which wasn't used anyway.
• Slightly change the $SAGE_LOCAL/bin/Singular script, use "$@" instead of $*.
• Remove workaround for GCC-4.0.x on Darwin (obsolete by the GCC spkg).
• Fix formatting of spkg-install (consistent indentation, no TABs).

Upstream bugs discovered:

• ​#437: negate() should be NTL::negate() (little feedback)
• ​#438: Singular configured --without-debug doesn't build (developers acknowledge the bug)
• ​#439: factorize() returns wrong constant (fixed upstream, but not in a stable release)
• ​#440: Factoring over a finite field returns reducible factor (fixed upstream, but not in a stable release)

[leif]

checking for FLINT >= 2.3... not found
configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use --with-flint=PATH_TO_DIR_CONTAINING_LIB_AND_INCLUDE (see also ./configure --help if you do not understand what we are talking about)

:P

And lots of other warnings...

[leif]

Replying to leif:

And lots of other warnings...

These are the ones I get from configure and config.status:

configure: warning: Building of doc might fail. Need Texinfo
configure: WARNING: unrecognized options: --with-apint, --with-ntl, --without-MP, --without-lex, --without-bison, --without-Boost, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-factory, --with-libfac
configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use --with-flint=PATH_TO_DIR_CONTAINING_LIB_AND_INCLUDE (see also ./configure --help if you do not understand what we are talking about)
config.status: WARNING:  'GNUmakefile.in' seems to ignore the --datarootdir setting
configure: WARNING: unrecognized options: --with-apint, --with-ntl, --without-MP, --without-lex, --without-bison, --without-Boost, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-factory, --with-libfac
configure: warning: factory.h not found! Install factory before building libfac!
configure: WARNING: unrecognized options: --with-gmp, --with-ntl, --without-bison, --enable-gmp, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-Singular
configure: WARNING: building without lex -- make might fail
configure: WARNING: building without python support
configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use --with-flint=PATH_TO_DIR_CONTAINING_LIB_AND_INCLUDE (see also ./configure --help if you do not understand what we are talking about)
configure: WARNING: unrecognized options: --with-gmp, --with-ntl, --without-bison, --enable-gmp, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-Singular
configure: warning: Building of doc might fail. Need Texinfo
configure: WARNING: unrecognized options: --with-apint, --with-ntl, --without-MP, --without-lex, --without-bison, --without-Boost, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-factory, --with-libfac
configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use --with-flint=PATH_TO_DIR_CONTAINING_LIB_AND_INCLUDE (see also ./configure --help if you do not understand what we are talking about)
config.status: WARNING:  'GNUmakefile.in' seems to ignore the --datarootdir setting
configure: WARNING: unrecognized options: --with-apint, --with-ntl, --without-MP, --without-lex, --without-bison, --without-Boost, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-factory, --with-libfac
configure: warning: factory.h not found! Install factory before building libfac!
configure: WARNING: unrecognized options: --with-gmp, --with-ntl, --without-bison, --enable-gmp, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-Singular
configure: WARNING: building without lex -- make might fail
configure: WARNING: building without python support
configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use --with-flint=PATH_TO_DIR_CONTAINING_LIB_AND_INCLUDE (see also ./configure --help if you do not understand what we are talking about)
configure: WARNING: unrecognized options: --with-gmp, --with-ntl, --without-bison, --enable-gmp, --enable-Singular, --enable-factory, --enable-libfac, --enable-IntegerProgramming, --disable-doc, --with-malloc, --disable-debug, --enable-omalloc, --with-external-config_h, --with-track-custom, --enable-Plural, --with-Singular
configure: WARNING: unrecognized options: --with-apint, --with-ntl, --disable-debug
configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use --with-flint=PATH_TO_DIR_CONTAINING_LIB_AND_INCLUDE (see also ./configure --help if you do not understand what we are talking about)
config.status: WARNING:  'GNUmakefile.in' seems to ignore the --datarootdir setting
configure: WARNING: unrecognized options: --with-apint, --with-ntl, --disable-debug

The unrecognized options should be addressed I think.

No idea how to interpret "factory.h not found! Install factory before building libfac!", as the build succeeded.

"Building without python support" can safely be ignored I guess, as we use our own Cython wrappers.

[jdemeyer]

Replying to leif:

The unrecognized options should be addressed I think.

I fixed the fixable warnings. Many of them are caused by recursive calling of configure, for example, the top-level configure calls omalloc/configure. Many options are supported by some (but not all) configure scripts. These will give warnings and I don't see how to avoid these.

[leif]

I assume that this is work in progress (i.e., you haven't tried to fix doctest errors yet).

Anyway, here's what I got on Ubuntu 10.04.4 LTS x86_64, with Sage 5.2.rc0 and GCC 4.7.0:

The following tests failed:

	sage -t  --long -force_lib devel/sage/doc/en/constructions/polynomials.rst # 1 doctests failed
	sage -t  --long -force_lib devel/sage/sage/rings/function_field/function_field.py # 1 doctests failed
	sage -t  --long -force_lib devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx # 3 doctests failed
	sage -t  --long -force_lib devel/sage/sage/rings/polynomial/multi_polynomial_ideal.py # 1 doctests failed
	sage -t  --long -force_lib devel/sage/sage/calculus/wester.py # 1 doctests failed
	sage -t  --long -force_lib devel/sage/sage/libs/singular/function.pyx # 2 doctests failed
	sage -t  --long -force_lib devel/sage/sage/combinat/words/words.py # 0 doctests failed

(The last failure was a segfault with a large traceback IIRC. Somewhat surprisingly successfully compiled with -O3, although many if not most compile commands override this by -O2; looks as if they use CPPFLAGS instead of CXXFLAGS in some parts.)

Let me know in case you're interested in further output; I guess you can reproduce most of the errors.

[jdemeyer]

Replying to leif:

I assume that this is work in progress (i.e., you haven't tried to fix doctest errors yet).

Exactly, I mainly worked on spkg-install.

[jdemeyer]

This is a new bug, the new answer is incorrect:

sage -t  --long -force_lib devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx
**********************************************************************
File "/release/merger/sage-5.2.rc1/devel/sage-main/sage/rings/polynomial/multi_polynomial_libsingular.pyx", line 3856:
    sage: p.factor()
Expected:
    (-2*v^2*u + 4*u^3 + v^2)^2
Got:
    (4) * (-2*v^2*u + 4*u^3 + v^2)^2
**********************************************************************

[leif]

Replying to jdemeyer:

This is a new bug, the new answer is incorrect:

Expected:
    (-2*v^2*u + 4*u^3 + v^2)^2
Got:
    (4) * (-2*v^2*u + 4*u^3 + v^2)^2

Yes, the most obvious one... :-)

Just noticed the failure in words.py apparently isn't reproducible. Traceback was

${SAGE_LOCAL}/lib/libcsage.so(print_backtrace+0x31)[0x2abd9e8f6664]
${SAGE_LOCAL}/lib/libcsage.so(sigdie+0x14)[0x2abd9e8f6696]
${SAGE_LOCAL}/lib/libcsage.so(sage_signal_handler+0x218)[0x2abd9e8f6250]
/lib/libpthread.so.0(+0xf8f0)[0x2abd9c9158f0]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(+0x135020)[0x2abd9c628020]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(+0x76aa7)[0x2abd9c569aa7]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(+0x1352b7)[0x2abd9c6282b7]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(_PyObject_GC_Malloc+0x115)[0x2abd9c6292b5]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(_PyObject_GC_New+0xd)[0x2abd9c6292ed]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(PyCFunction_NewEx+0xc5)[0x2abd9c584f05]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(Py_InitModule4_64+0x140)[0x2abd9c60bc60]
${SAGE_LOCAL}/lib/python/site-packages/numpy/core/multiarray.so(initmultiarray+0x2b)[0x2abdcd07186b]
${SAGE_LOCAL}/lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x99)[0x2abd9c6073b9]
...
Segmentation fault

[jdemeyer]

Another Singular bug:

sage -t --long "devel/sage/sage/rings/function_field/function_field.py"
**********************************************************************
File "/release/merger/sage-5.2.rc1/devel/sage/sage/rings/function_field/function_field.py", line 1132:
    sage: f.factor()
Expected:
    (1/t) * (X + 3*t) * (X + 5*t) * (X + 6*t) * (X^2 + 1/t) * (X^2 + 6/t)
Got:
    (1/t) * (X + 3*t) * (X + 5*t) * (X + 6*t) * (X^4 + 6/t^2)
**********************************************************************

Reported upstream at ​http://www.singular.uni-kl.de:8002/trac/ticket/440.

[jdemeyer]

New spkg, adds fixes for Singular bugs 439 and 440.