Opened 7 years ago
Closed 7 years ago
#13237 closed enhancement (fixed)
Upgrade Singular
Reported by:  jdemeyer  Owned by:  tbd 

Priority:  critical  Milestone:  sage5.4 
Component:  packages: standard  Keywords:  Singular spkg 
Cc:  fbissey, malb, jpflori  Merged in:  sage5.4.beta0 
Authors:  Jeroen Demeyer, Alexander Dreyer, Dmitrii Pasechnik, KarlDieter Crisman, JeanPierre Flori  Reviewers:  Alexander Dreyer, François Bissey 
Report Upstream:  None of the above  read trac for reasoning.  Work issues:  
Branch:  Commit:  
Dependencies:  Stopgaps: 
Description (last modified by )
Upgrade Singular to version 315 (released 12 July 2012).
Upstream bugs discovered:
 #437: negate() should be NTL::negate() (upstream needs testers)
 #438: Singular configured withoutdebug doesn't build ("fixed" by removing the option)
 #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)
 #441: Factoring over a finite field sometimes returns wrong result (fixed upstream, but not in a stable release)
 #443: configure should check for nanosleep in lrt (fixed upstream, but not in a stable release)
This new version fixes #13129, #12918, #12928, #12846, #12089, #13344.
Apply 13237_singular_3_1_5.patch and 13237_tests.patch to the Sage library.
New spkg: http://boxen.math.washington.edu/home/jdemeyer/spkg/singular315.p1.spkg
singular315.p1 (Simon King, 29 August 2012)
 Trac #13237: add patch install_table.patch
singular315.p0 (Jeroen Demeyer, Alexander Dreyer, 10 August 2012)
 Trac #13237: Upgrade to version 315.
 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
 In spkginstall, simplify apply_patches(), automatically apply all patches in patches/*.patch, move conditional patches to patches/conditional
 Rename some patches such that they all have the extension '.patch'
 Put the two patches for SAGE_DEBUG (Singular.Makefile.in.debug.patch and kernel.Makefile.in.debug.patch) into one file conditional/sage_debug.patch.
 Add several patches (see above):
 NTL_negate.patch
 singular_trac_439.patch
 singular_trac_440.patch
 singular_trac_441.patch
 singular_trac_443.patch
 sage_trac_12089.patch
 slibdir.patch
 When building Singular, don't first make install and then make installnolns. Instead, only do the latter.
 Don't create the LIB>lib symlink, which is no longer needed.
 In spkginstall, remove distclean() step; merge clean_headers() and part of the old distclean() into remove_old_version().
 Only unset LD on Darwin.
 Remove the unsetting of TMPDIR (bug fixed upstream).
 Do not override userset CFLAGS and CXXFLAGS.
 Echo all error messages to stderr instead of stdout.
 Fix various ./configure options and remove some unsupported options.
 Always configure withdebug, as withoutdebug doesn't work, see http://www.singular.unikl.de:8002/trac/ticket/438
 Don't create sage_singular symlink, which wasn't used anyway.
 Replace the $SAGE_LOCAL/bin/Singular script by a symlink.
 Remove workaround for GCC4.0.x on Darwin (obsolete by the GCC spkg).
 Fix formatting of spkginstall (consistent indentation, no TABs).
Attachments (4)
Change History (92)
comment:1 Changed 7 years ago by
 Description modified (diff)
 Keywords spkg added
comment:2 Changed 7 years ago by
 Description modified (diff)
comment:3 Changed 7 years ago by
 Cc fbissey added
comment:4 Changed 7 years ago by
 Cc malb added
 Description modified (diff)
 Keywords Singular added
comment:5 Changed 7 years ago by
 Description modified (diff)
comment:6 followup: ↓ 7 Changed 7 years ago by
comment:7 in reply to: ↑ 6 ; followup: ↓ 8 Changed 7 years ago by
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: withapint, withntl, withoutMP, withoutlex, withoutbison, withoutBoost, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withfactory, withlibfac configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use withflint=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: withapint, withntl, withoutMP, withoutlex, withoutbison, withoutBoost, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withfactory, withlibfac configure: warning: factory.h not found! Install factory before building libfac! configure: WARNING: unrecognized options: withgmp, withntl, withoutbison, enablegmp, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withSingular 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 withflint=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: withgmp, withntl, withoutbison, enablegmp, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withSingular configure: warning: Building of doc might fail. Need Texinfo configure: WARNING: unrecognized options: withapint, withntl, withoutMP, withoutlex, withoutbison, withoutBoost, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withfactory, withlibfac configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use withflint=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: withapint, withntl, withoutMP, withoutlex, withoutbison, withoutBoost, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withfactory, withlibfac configure: warning: factory.h not found! Install factory before building libfac! configure: WARNING: unrecognized options: withgmp, withntl, withoutbison, enablegmp, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withSingular 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 withflint=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: withgmp, withntl, withoutbison, enablegmp, enableSingular, enablefactory, enablelibfac, enableIntegerProgramming, disabledoc, withmalloc, disabledebug, enableomalloc, withexternalconfig_h, withtrackcustom, enablePlural, withSingular configure: WARNING: unrecognized options: withapint, withntl, disabledebug configure: WARNING: Unable to find FLINT (which is strongly recommended) on your machine: please use withflint=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: withapint, withntl, disabledebug
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.
comment:8 in reply to: ↑ 7 Changed 7 years ago by
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 toplevel 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.
comment:9 Changed 7 years ago by
 Description modified (diff)
comment:10 followup: ↓ 11 Changed 7 years ago by
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.
comment:11 in reply to: ↑ 10 Changed 7 years ago by
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 spkginstall
.
comment:12 followup: ↓ 13 Changed 7 years ago by
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/sage5.2.rc1/devel/sagemain/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 **********************************************************************
comment:13 in reply to: ↑ 12 Changed 7 years ago by
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/sitepackages/numpy/core/multiarray.so(initmultiarray+0x2b)[0x2abdcd07186b] ${SAGE_LOCAL}/lib/libpython2.7.so.1.0(_PyImport_LoadDynamicModule+0x99)[0x2abd9c6073b9] ... Segmentation fault
comment:14 Changed 7 years ago by
 Description modified (diff)
comment:15 Changed 7 years ago by
 Description modified (diff)
Another Singular bug:
sage t long "devel/sage/sage/rings/function_field/function_field.py" ********************************************************************** File "/release/merger/sage5.2.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.unikl.de:8002/trac/ticket/440.
comment:16 Changed 7 years ago by
 Description modified (diff)
comment:17 Changed 7 years ago by
 Description modified (diff)
 Report Upstream changed from N/A to None of the above  read trac for reasoning.
New spkg, adds fixes for Singular bugs 439 and 440.
comment:18 Changed 7 years ago by
 Description modified (diff)
comment:19 Changed 7 years ago by
 Description modified (diff)
comment:20 Changed 7 years ago by
Reproducible doctest failure:
********************************************************************** File "/release/merger/sage5.3.beta0/devel/sagemain/sage/libs/singular/function.pyx", line 1569: sage: singular_list(2, 3, 6, ring=P) Exception raised: Traceback (most recent call last): File "/release/merger/sage5.3.beta0/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/release/merger/sage5.3.beta0/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/release/merger/sage5.3.beta0/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_72[16]>", line 1, in <module> singular_list(Integer(2), Integer(3), Integer(6), ring=P)###line 1569: sage: singular_list(2, 3, 6, ring=P) File "function.pyx", line 1248, in sage.libs.singular.function.SingularFunction.__call__ (sage/libs/singular/function.cpp:11875) return call_function(self, args, ring, interruptible, attributes) File "function.pyx", line 1438, in sage.libs.singular.function.call_function (sage/libs/singular/function.cpp:13425) raise RuntimeError("Error in Singular function call '%s':\n%s"%(self._name, RuntimeError: Error in Singular function call 'list': list(`int`,`int`,`int`) failed ********************************************************************** File "/release/merger/sage5.3.beta0/devel/sagemain/sage/libs/singular/function.pyx", line 1585: sage: singular_list((1,2,3),3,[1,2,3], ring=P) Exception raised: Traceback (most recent call last): File "/release/merger/sage5.3.beta0/local/bin/ncadoctest.py", line 1231, in run_one_test self.run_one_example(test, example, filename, compileflags) File "/release/merger/sage5.3.beta0/local/bin/sagedoctest.py", line 38, in run_one_example OrigDocTestRunner.run_one_example(self, test, example, filename, compileflags) File "/release/merger/sage5.3.beta0/local/bin/ncadoctest.py", line 1172, in run_one_example compileflags, 1) in test.globs File "<doctest __main__.example_72[26]>", line 1, in <module> singular_list((Integer(1),Integer(2),Integer(3)),Integer(3),[Integer(1),Integer(2),Integer(3)], ring=P)###line 1585: sage: singular_list((1,2,3),3,[1,2,3], ring=P) File "function.pyx", line 1248, in sage.libs.singular.function.SingularFunction.__call__ (sage/libs/singular/function.cpp:11875) return call_function(self, args, ring, interruptible, attributes) File "function.pyx", line 1438, in sage.libs.singular.function.call_function (sage/libs/singular/function.cpp:13425) raise RuntimeError("Error in Singular function call '%s':\n%s"%(self._name, RuntimeError: Error in Singular function call 'list': list(`intvec`,`int`,`list`) failed **********************************************************************
Nonreproducible doctest failure:
********************************************************************** File "/release/merger/sage5.3.beta0/devel/sagemain/sage/rings/polynomial/multi_polynomial_libsingular.pyx", line 3921: sage: f.factor() Expected: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + (a)*x^8 + (a)*y^4) Got: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + (a + 1)*x^8 + (a + 1)*y^4) **********************************************************************
comment:21 followup: ↓ 22 Changed 7 years ago by
So far I only tested the files that previously failed for me (with the new spkg and the Sage library patch applied).
I get the same list()
errors (although prepended by some debug output it seems, before the doctest error is printed), and sporadically the f.factor()
error  with varying results:
sage t long force_lib "devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx" ********************************************************************** File "${SAGE_ROOT}/devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx", line 3910: sage: f.factor() Expected: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + (a)*x^8 + (a)*y^4) Got: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + (a + 1)*x^8 + (a + 1)*y^4) ********************************************************************** 1 items had failures: 1 of 86 in __main__.example_77 ***Test Failed*** 1 failures. sage t long force_lib "devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx" ********************************************************************** File "${SAGE_ROOT}/devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx", line 3910: sage: f.factor() Expected: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + (a)*x^8 + (a)*y^4) Got: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9) ********************************************************************** 1 items had failures: 1 of 86 in __main__.example_77 ***Test Failed*** 1 failures. sage t long force_lib "devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx" ********************************************************************** File "${SAGE_ROOT}/devel/sage/sage/rings/polynomial/multi_polynomial_libsingular.pyx", line 3910: sage: f.factor() Expected: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + (a)*x^8 + (a)*y^4) Got: x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + x^8 + y^4) ********************************************************************** 1 items had failures: 1 of 86 in __main__.example_77 ***Test Failed*** 1 failures.
(For me it's line 3910; presumably due to some other patch. The first variant seems to occur more often. All tests run sequentially, FWIW.)
P.S.: Run 100 times from the shell, the test failed 51 times.
comment:22 in reply to: ↑ 21 Changed 7 years ago by
Replying to leif:
P.S.: Run 100 times from the shell, the test failed 51 times.
(Running sage t ...
in a for
loop.)
25x x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + (a + 1)*x^8 + (a + 1)*y^4) 15x x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9 + x^8 + y^4) 11x x * y^3 * (y^8 + (a)*y^7 + (a + 1)*x) * (x^7*y^3 + x*y^9)
comment:23 Changed 7 years ago by
 Description modified (diff)
Nonreproducible factoring bug reported upstream: http://www.singular.unikl.de:8002/trac/ticket/441
comment:24 Changed 7 years ago by
New patch fixes all doctest errors (except for the upstream factoring bug).
comment:25 Changed 7 years ago by
 Description modified (diff)
comment:26 Changed 7 years ago by
 Description modified (diff)
comment:27 Changed 7 years ago by
 Description modified (diff)
comment:28 Changed 7 years ago by
 Status changed from new to needs_review
I added a patch for Singular Trac 441 (which is in the git sources, even though Trac hasn't been updated yet).
Needs review (the spkg will be committed after positive_review if that's okay).
comment:29 Changed 7 years ago by
 Description modified (diff)
comment:30 Changed 7 years ago by
 Description modified (diff)
comment:31 Changed 7 years ago by
 Description modified (diff)
comment:32 Changed 7 years ago by
 Description modified (diff)
comment:33 Changed 7 years ago by
 Cc jpflori added
comment:34 Changed 7 years ago by
spkg and patch apply/install fine. Also the tests are fine. So I'm close to a positive review, just waiting for the patch from #12089.
comment:35 followups: ↓ 36 ↓ 52 Changed 7 years ago by
Just for the record: Did pass ptestlong
(with a bit of luck, cf. the "random" factoring) with Sage 5.2[.rc0] (Ubuntu 10.04.4 LTS x86_64, FSF GCC 4.7.0, with O3
, see above).
Patch applies to Sage 5.3.beta0 as well (a few lines offset, never mind).
Only just noticed that old installations get removed before we even attempt to build the new one; this should in general only be done if the build succeeded.
(Haven't yet closely looked at [the changes to] spkginstall
.)
comment:36 in reply to: ↑ 35 Changed 7 years ago by
Replying to leif:
Patch applies to Sage 5.3.beta0 as well (a few lines offset, never mind).
ptestlong
also passed without errors, but took longer than usual (despite the machine being otherwise idle).
comment:37 followup: ↓ 38 Changed 7 years ago by
It would be nice to fix #13344 as well in this ticket. Hopefully the problem should be tracked down quite quickly.
comment:38 in reply to: ↑ 37 ; followup: ↓ 39 Changed 7 years ago by
 Status changed from needs_review to needs_work
Replying to jpflori:
It would be nice to fix #13344 as well in this ticket. Hopefully the problem should be tracked down quite quickly.
yes, I can confirm that installing this spkg on MacOSX one gets Singular LIB files into SAGELOCAL/lib/
, as well as in the right place, i.e. SAGELOCAL/share/singular/
, which is certainly not what one would want.
comment:39 in reply to: ↑ 38 Changed 7 years ago by
Replying to dimpase:
yes, I can confirm that installing this spkg on MacOSX one gets Singular LIB files into
SAGELOCAL/lib/
, as well as in the right place, i.e.SAGELOCAL/share/singular/
, which is certainly not what one would want.
It think the best solution would be to replace $MAKE
by "$MAKE slibdir=$SAGE_LOCAL/share/singular" in the spkg.
comment:40 Changed 7 years ago by
Or maybe "$MAKE slibdir=\"$SAGE_LOCAL/share/singular\""
?
comment:41 Changed 7 years ago by
@jdemeyer I could take care for the changes, if you don't mind?
comment:42 Changed 7 years ago by
Just in case (won't have time tomorrow), I was so free to propose a changed spkg here: http://boxen.math.washington.edu/home/dreyer/spkg/singular315.p0.spkg
As before, the changes are not committed yet. Also I haven't changes the URL in the description, as Jeroen might continue with other fixes.
The changes are as follows (for review):

singular315.p0.
old new 9 9 diff r 1275ac543b53 SPKG.txt 10 10  a/SPKG.txt Sat Mar 17 11:18:23 2012 +0100 11 11 +++ b/SPKG.txt Sun Aug 05 22:36:36 2012 +0200 12 @@ 30,14 +30,1 7@@12 @@ 30,14 +30,19 @@ 13 13 See spkgchanges for how to delete unnecessary stuff under src/ 14 14 15 15 Several patches are applied. … … 32 32 + http://www.singular.unikl.de:8002/trac/ticket/440 33 33 + * singular_trac_441.patch: fix taken from upstream for 34 34 + http://www.singular.unikl.de:8002/trac/ticket/441 35 + * sage_trac_12089.patch: fix (also reported upstream) from 36 + https://github.com/alexanderdreyer/SingularSources/commit/7902222 35 37 36 38 Other notes 37 39 * The option 'withoutdynamickernel' is used on *all* 38 @@ 51,9 +5 4,51@@40 @@ 51,9 +56,54 @@ 39 41 investigated as a possible cause later. 40 42 * Be sure that Singular/Singular.rc.in is present, as occasionally this 41 43 was missing, which caused problems on Cygwin (e.g., see #10235) … … 49 51 50 52 == ChangeLog == 51 53 52 +=== singular315.p0 (Jeroen Demeyer, 2August 2012) ===54 +=== singular315.p0 (Jeroen Demeyer, 5 August 2012) === 53 55 + * Trac #13237: Upgrade to version 315. 54 56 + * Removed patches which are now upstreamed: 55 57 +  patches/Singular.Makefile.in.shared.patch … … 70 72 +  singular_trac_439.patch 71 73 +  singular_trac_440.patch 72 74 +  singular_trac_441.patch 75 +  sage_trac_12089.patch 73 76 + * In spkginstall, remove distclean() step; merge clean_headers() and 74 77 + part of the old distclean() into remove_old_version(). 78 + * In spkginstall, added slibdir="$SAGE_LOCAL/share/singular" to 79 + $MAKE installlibsingular . 75 80 + * Only unset LD on Darwin. 76 81 + * Remove the unsetting of TMPDIR (bug fixed upstream). 77 82 + * Do not override userset CFLAGS and CXXFLAGS. … … 6812 6817  #if defined(ix86Mac_darwin) 6813 6818  #define HAVE_ELF_SYSTEM 6814 6819  #endif 6820 diff r 1275ac543b53 patches/sage_trac_12089.patch 6821  /dev/null Thu Jan 01 00:00:00 1970 +0000 6822 +++ b/patches/sage_trac_12089.patch Sun Aug 05 22:36:36 2012 +0200 6823 @@ 0,0 +1,29 @@ 6824 +From 7902222c6e73d452b3d75576bd9bc0140f5e827a Mon Sep 17 00:00:00 2001 6825 +From: Alexander Dreyer <alexander.dreyer@itwm.fraunhofer.de> 6826 +Date: Sat, 4 Aug 2012 21:53:32 +0200 6827 +Subject: [PATCH] fix: apply LDFLAGS fixes from svn#13210/git#b1dfafe to cygwinspecific flags (Sage's trac #12089; reported by JeanPierre Flori) 6828 + 6829 + 6830 + Singular/Makefile.in  6 +++ 6831 + 1 files changed, 3 insertions(+), 3 deletions() 6832 + 6833 +diff git a/Singular/Makefile.in b/Singular/Makefile.in 6834 +index c4a6e78..b907085 100644 6835 + a/Singular/Makefile.in 6836 ++++ b/Singular/Makefile.in 6837 +@@ 90,9 +90,9 @@ LDFLAGSG = L@prefix@/kernel L../kernel lkernel_g @LD_DYN_FLAGS1@ @LDFLAGS@ 6838 + LDFLAGSP = L@prefix@/kernel L../kernel lkernel_p @LD_DYN_FLAGS1@ @LDFLAGS@ 6839 + else 6840 + ## L/usr/local/lib L@prefix@/modules/python > PySingular 6841 +LDFLAGS = L@prefix@/kernel L/bin lkernel @LDFLAGS@ L/usr/local/lib L../modules/python 6842 +LDFLAGSG = L@prefix@/kernel L/bin lkernel_g @LDFLAGS@ 6843 +LDFLAGSP = L@prefix@/kernel L/bin lkernel_p @LDFLAGS@ 6844 ++LDFLAGS = L@prefix@/kernel L../kernel L/bin lkernel @LDFLAGS@ L/usr/local/lib L../modules/python 6845 ++LDFLAGSG = L@prefix@/kernel L../kernel L/bin lkernel_g @LDFLAGS@ 6846 ++LDFLAGSP = L@prefix@/kernel L../kernel L/bin lkernel_p @LDFLAGS@ 6847 + endif 6848 + LD_DYN_FLAGS1 = @LD_DYN_FLAGS1@ 6849 + LD_DYN_FLAGS2 = @LD_DYN_FLAGS2@ 6850 + 6851 +1.6.0.2 6852 + 6815 6853 diff r 1275ac543b53 patches/sing_win.cc.diff 6816 6854  a/patches/sing_win.cc.diff Sat Mar 17 11:18:23 2012 +0100 6817 6855 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 … … 7330 7368 + config  return $? 7331 7369 7332 7370 $MAKE clean 7333 $MAKE installlibsingular 7371  $MAKE installlibsingular 7372 + $MAKE slibdir="$SAGE_LOCAL/share/singular" installlibsingular 7334 7373 7335 7374 if [ $? ne 0 ]; then 7336 7375  echo "Unable to install libsingular."
comment:43 Changed 7 years ago by
comment:44 Changed 7 years ago by
For the slibdir issue, I am patching Makefile.in instead, I think this is the best solution.
comment:45 Changed 7 years ago by
comment:46 Changed 7 years ago by
 Description modified (diff)
 Status changed from needs_work to needs_review
comment:47 Changed 7 years ago by
 Description modified (diff)
comment:48 followup: ↓ 49 Changed 7 years ago by
Just nitpicking: there a typo in my name.
comment:49 in reply to: ↑ 48 Changed 7 years ago by
comment:50 Changed 7 years ago by
 Status changed from needs_review to needs_work
comment:51 followup: ↓ 53 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:52 in reply to: ↑ 35 Changed 7 years ago by
Replying to leif:
Only just noticed that old installations get removed before we even attempt to build the new one; this should in general only be done if the build succeeded.
Unfortunately, Singular doesn't have separate build
and install
targets. So building and installing must happen together.
comment:53 in reply to: ↑ 51 ; followup: ↓ 54 Changed 7 years ago by
Replying to jdemeyer: I can confirm that the latest spkg installs cleanly on MacOSX 10.6.8 and on Cygwin.
comment:54 in reply to: ↑ 53 Changed 7 years ago by
comment:55 Changed 7 years ago by
 Description modified (diff)
 Status changed from needs_review to needs_work
This doesn't build on Solaris: http://www.singular.unikl.de:8002/trac/ticket/443
comment:56 Changed 7 years ago by
Hannes Schönemann of the Singular team has provided a patch for this: https://github.com/Singular/Sources/commit/cf39407a525018da4baffd05e88315bd83075f8c.patch
comment:57 Changed 7 years ago by
 Description modified (diff)
 Status changed from needs_work to needs_review
Seems to build fine on Solaris now, needs review again.
comment:58 Changed 7 years ago by
Installs and tests sage/rings without any problems. So positive review from my side.
comment:59 Changed 7 years ago by
 Reviewers set to Alexander Dreyer
comment:60 Changed 7 years ago by
Anybody willing to fully review this ticket?
comment:61 followup: ↓ 62 Changed 7 years ago by
 Reviewers changed from Alexander Dreyer to Alexander Dreyer, François Bissey
 Status changed from needs_review to positive_review
I will push the button. There is a lot of clean up and of course new issues (like one of my colleagues says: exchange old bugs for new ones). I looked carefully at all the changes in spkginstall (make that very carefully for the last 2 days  but I could still have missed something) and am happy with them. Happy with the new patches too.
comment:62 in reply to: ↑ 61 Changed 7 years ago by
Replying to fbissey:
I looked carefully at all the changes in spkginstall (make that very carefully for the last 2 days  but I could still have missed something) and am happy with them. Happy with the new patches too.
Thanks a lot for this.
comment:63 Changed 7 years ago by
That's annoying now that I have pushed the button I found something (that obviously is not impacting sage) that should be reported upstream. The header factory/assert.h is not installed and it is included in factory/templates/ftmpl_{matrix,array,list}.cc. I don't think there are anymore missing headers.
comment:64 followup: ↓ 65 Changed 7 years ago by
Spoke too soon from factory/templates/ftmpl_inst.cc
#include "canonicalform.h" #include "cf_map.h" #include "cf_reval.h"
None of these are installed either.
comment:65 in reply to: ↑ 64 Changed 7 years ago by
Replying to fbissey: Thanks for the hint, I just reported that upstream: http://www.singular.unikl.de:8002/trac/ticket/446
comment:66 Changed 7 years ago by
Just to be clear. I don't think we should delay this ticket for these headers. If there was an effect on sage we would know by now. But we should definitely have a follow up ticket to pick any upstream patch. Thanks Alexander I was counting on you picking it up :).
comment:67 Changed 7 years ago by
 Milestone changed from sage5.3 to sage5.4
comment:68 followup: ↓ 69 Changed 7 years ago by
comment:69 in reply to: ↑ 68 Changed 7 years ago by
 Status changed from positive_review to needs_work
Replying to zimmerma:
I'd like to see nonregression tests in this patch, for all tickets solved by this one: #13129, #12918, #12928, #12846, #12089, #13344.
Good suggestion, however #12089, #13344 are about compiling Singular so I don't think we should add a regression test for that (the real test is just checking that any upgrades don't break the build). Then #12846 is also tricky because it is about a computation which randomly runs slow or gets stuck.
For the other 3 tickets, we should indeed add a regression test. I'll take care of the patch.
comment:70 Changed 7 years ago by
We could test existence of *.lib files in the LIB directory for #13344, or of $SAGE_LOCAL/LIB directory. The problem is critical on Cygwin where LIB resolves to lib and messes PyOpenSSL compilation (although that package won't be built anymore soon), but was also present on every platform.
I agree that #12089 cannot really be tested, except for the fact that Singular succeeded to build.
comment:71 Changed 7 years ago by
sorry I meant I'd like to see nonregression tests if possible. Thank you Jeroen for taking care of them.
Paul
comment:72 followup: ↓ 73 Changed 7 years ago by
 Description modified (diff)
 Priority changed from major to critical
 Status changed from needs_work to needs_review
Additional patch 13237_tests.patch needs review.
comment:73 in reply to: ↑ 72 Changed 7 years ago by
 Status changed from needs_review to positive_review
Replying to jdemeyer:
Additional patch 13237_tests.patch needs review.
Indeed, I can confirm that the tests check for recurrence of the solved problems.
comment:74 followup: ↓ 75 Changed 7 years ago by
There is a small thing that I'd like to change: There is a header table.h, that is currently not installed. However, it is needed by libsing (not libsingular).
libsing is a package allowing GAP to use Singular natively. I don't know if it would be of general interest to have it in Sage. Anyway: Should there be a new ticket for the installation of table.h, or should it be done here?
comment:75 in reply to: ↑ 74 ; followup: ↓ 78 Changed 7 years ago by
Replying to SimonKing:
There is a small thing that I'd like to change: There is a header table.h, that is currently not installed. However, it is needed by libsing (not libsingular).
libsing is a package allowing GAP to use Singular natively. I don't know if it would be of general interest to have it in Sage. Anyway: Should there be a new ticket for the installation of table.h, or should it be done here?
I think this is not related tot he upgrade, so this should be a feature request to the Singularteam. But of course, any resulting patch could be integrated in the next spkg eventually.
comment:76 followup: ↓ 77 Changed 7 years ago by
It seems to me that the spkg contains uncommitted changes.
comment:77 in reply to: ↑ 76 Changed 7 years ago by
Replying to SimonKing:
It seems to me that the spkg contains uncommitted changes.
You are very right, I forgot to do sage pkg
after committing the changes. Should be fixed now.
comment:78 in reply to: ↑ 75 Changed 7 years ago by
Replying to AlexanderDreyer:
Replying to SimonKing: I think this is not related tot he upgrade,
Granted. But if we upgrade Singular anyway, we could as well use a little patch that installs just one additional header.
so this should be a feature request to the Singularteam. But of course, any resulting patch could be integrated in the next spkg eventually.
Here is the suggested change, anyway. Add a file patches/install_table.patch containing
 src/Singular/Makefile.in 20120711 11:00:13.000000000 +0100 +++ src/Singular/Makefile.in 20120827 16:22:26.013159361 +0100 @@ 599,7 +599,7 @@ ${INSTALL_PROGRAM} $$file ${libdir}; \ done ${INSTALL_PROGRAM} libsingular.h ${includedir}  for file in subexpr.h tok.h grammar.h ipid.h lists.h ipshell.h attrib.h; do \ + for file in subexpr.h tok.h grammar.h ipid.h lists.h ipshell.h attrib.h table.h; do \ sed e "s:<kernel/:<singular/:" < $$file sed e "s:<Singular/:<singular/:"sed e "s:<omalloc/:<:"sed e "s:<factory/:<:" >${includedir}/singular/$$file ;\ done
comment:79 followup: ↓ 80 Changed 7 years ago by
I agree with AlexanderDreyer that you should make a request to upstream for table.h
to be installed. If the patch gets accepted upstream, it will also be easier to review this ticket.
comment:80 in reply to: ↑ 79 Changed 7 years ago by
Replying to jdemeyer:
I agree with AlexanderDreyer that you should make a request to upstream for
table.h
to be installed. If the patch gets accepted upstream, it will also be easier to review this ticket.
I asked Hans Schönemann today, and he answered: "Meinetwegen."
In English, I guess that's: "I don't mind."
comment:81 Changed 7 years ago by
 Description modified (diff)
 Status changed from positive_review to needs_work
comment:82 followup: ↓ 83 Changed 7 years ago by
 Status changed from needs_work to needs_review
comment:83 in reply to: ↑ 82 Changed 7 years ago by
 Status changed from needs_review to positive_review
Replying to jdemeyer: I'll give a positive review to this (was discussed before),
comment:84 Changed 7 years ago by
One questions regarding Alexander's comment on #7797: Has it really been the case on Solaris SPARC that an outdated Singular/tok.h was hanging around? And if the answer is yes, a second question: Has the new singular spkg not properly installed the new one?
comment:85 followup: ↓ 86 Changed 7 years ago by
I am currently doing a complete build from scratch on Solaris SPARC with the new Singular to find out what's going on.
comment:86 in reply to: ↑ 85 ; followup: ↓ 87 Changed 7 years ago by
Replying to jdemeyer:
I am currently doing a complete build from scratch on Solaris SPARC with the new Singular to find out what's going on.
What came out of it?
comment:87 in reply to: ↑ 86 Changed 7 years ago by
comment:88 Changed 7 years ago by
 Merged in set to sage5.4.beta0
 Resolution set to fixed
 Status changed from positive_review to closed
:P
And lots of other warnings...