Re: Sage 8.2.beta3 released (R build failure)

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Vincent Delecroix

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Jan 18, 2018, 4:08:12 AM1/18/18
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On archlinux (gcc 7.2.1) I failed to build the R new package with the
recent upgrade to 8.2.beta3. See log attached.

On 18/01/2018 01:01, Volker Braun wrote:
> After reinstalling the OSX buildslave from scratch since the OSX 10.13
> upgrade resulted in a bootloop (why not let your customers beta-test the
> online migration to the new file system), we finally have a new release ;-)
>
>
> As always, you can get the latest beta version from the "develop" git
> branch. Alternatively, the self-contained source tarball is at
> http://www.sagemath.org/download-latest.html
>
>
> 56a4bc7e76 (tag: 8.2.beta3) Updated SageMath version to 8.2.beta3
> 048337c047 Trac #24395: Misc pip package upgrades
> 8609f7c782 Trac #24510: Function field factorization does not pass on proof
> parameter
> f5e3d11b3d Trac #24506: fix typos in the word construct
> 62c13d5b18 Trac #24502: Remove deprecated code from #17134
> 86fe6da505 Trac #24488: Iceland lost from the world
> a2e15560b8 Trac #24482: use https for matplotlib external links
> 21e1d6b007 Trac #24118: Add quick check for planarity
> 18f63eaa98 Trac #24530: some details in matrix_space
> f0ec00d4df Trac #24528: py3: wrap parameter of islice with int
> 3c212a0c7c Trac #24527: py3: remove one call to long in rand_seed
> f7e8b94eeb Trac #24520: py3: get rid of one __cmp__ in crypto
> d0a99f3570 Trac #24519: py3: richcmp for e_one_star
> 50bd6d6d5b Trac #24518: py3: richcmp for Unknown class
> 2148618254 Trac #24513: difference_family should return trooleans when
> existence=True
> c678add5e6 Trac #24509: little cleanup of alphabet
> 5b77075b84 Trac #24505: fixing some sphinx details in some refs
> d0ea961bc3 Trac #24504: small cleanup of cluster_algebra
> 4ed9afa846 Trac #24501: Hash of Integer broken on Python 3
> 22b6b73b9e Trac #24499: faster meet for Tamari lattice
> 05825d6856 Trac #24247: Implement __pow__ in the coercion model
> b2876696ea Trac #23297: Use faster Coxeter group for computing in the
> Iwahori-Hecke algebra
> f73bb1a6dc Trac #20222: One-off doctest failures in a fresh install because
> of matplotlib
> 81bcd75791 Trac #13979: Make CartesianProduct_iter a proper Parent
> 2968c818af Trac #23451: compiling linbox fails when /bin/sh is a recent dash
> 72afbd8f7c Trac #24498: clean-up of cluster complex
> 191d5a546b Trac #24496: Add Europe map graph
> 63e1ab20e4 Trac #24495: Graph and all_paths to non-existing vertex
> f2248bd51f Trac #24491: sdh_configure should use bash
> fc22d049a4 Trac #24486: get rid of CombinatorialClass in Restricted Growth
> Arrays
> d3a06a0e35 Trac #24485: get rid of CombinatorialClass in Necklaces
> 579b831d02 Trac #24480: is_cactus() fails for a non-outerplanar graph
> 9406f6171d Trac #24479: add hash to Tableaux classes
> d605d5fdbd Trac #24476: Support downloading of symlinked tarballs
> 229926a2fe Trac #24468: Fix unpickling old pickles of MeatAxe matrices
> 2001be9e53 Trac #24467: Refactor IntegerMulAction
> edd306a06d Trac #24444: Deprecate CoordinatePatch and DifferentialForm to
> keep a single version of differential forms
> e46891e4e0 Trac #24443: Replace is_Set() usage
> fc55e37bb2 Trac #24437: py3: minor fixes and cleanup of sage.sets.family
> 3b974324e7 Trac #24373: fix building Sage's Mac-app on OSX 10.13
> 0d1bcf2ab5 Trac #24261: py3: add py2 and py3 doctest flags
> a15ce54aa8 Trac #24234: py3: restore_atexit context manager
> e29baa4e70 Trac #24091: Bug in order of points on elliptic curves
> 5520e00bf2 Trac #23448: configure fails when run with a posix shell
> supporting $LINENO (e.g. dash 0.5.9 and many others)
> 378aff6289 Trac #24473: Remove edge_label() default parameter
> 4c50116420 Trac #24461: Simplify calling code in coercion_model.bin_op
> 59c8deb703 Trac #24446: Fix is_interval() on graphs
> 38f7b8559a Trac #24474: Run all tests in sage/combinat/root_system
> 2072f13213 Trac #24472: py3 adapt use of itertools.permutations
> 25f6982ab5 Trac #24471: Don't put non-built Cython extensions in
> sage_build_cython.extensions
> 6591a89e37 Trac #23685: Minkowski -> minkowski (polyhedra methods)
> ad6524d1f2 Trac #16613: fix content of polynomials
> 6d8cbd7b5e Trac #24470: py3: do not import replace
> 99c6482004 Trac #24466: Fix widget.descriprion
> fa30f8bfab Trac #24465: Let the completion functor prints the precision
> b843d59b60 Trac #24415: py3: fixes to sage.cpython.getattr
> 9ae0f035b4 Trac #24359: Turn MeatAxe into a dynamic library
> 7ae5f47caa Trac #24304: Make is_endomorphism_set be trivial for Endsets.
> 03bf86336c Trac #11982: Morphisms from elliptic curves to projective curves
> are not possible anymore
> 548223ad39 Trac #24445: Allow several implementations in random matrix
> a614b26cc4 Trac #24426: Fricas doctest failure
> 1f32f894c1 Trac #24464: ZZ is complete
> 7de729d3a1 Trac #24463: correct some typos
> db8e924bf5 Trac #24452: Add link in "PARI groups" doc page to PARI doc
> e2507193b9 Trac #24436: py3: fixes to sage.libs.symmetrica
> f767762e91 Trac #24420: Laurent power series fail unique representation
> c3eb6d17dd Trac #24413: make polynomial rings know that they are infinite
> e2b50f15d2 Trac #24216: Add crossing number of a graph
> 0b0486e154 Trac #24453: narrow_class_group: bug report
> 5b30357897 Trac #23426: Mac app fails to build
> f431ab27f1 Trac #24439: Avoid some performance problems in symbolics
> 612b904982 Trac #24306: Upgrade R to 3.4.3
> a1782046e2 (tag: 8.2.beta2) Updated SageMath version to 8.2.beta2
>
r-3.4.3.log

Vincent Delecroix

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Jan 18, 2018, 4:47:21 AM1/18/18
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I restart a build from scratch and I don't believe that R is responsible
in any way. This new build stopped on flint pointing at the same library
issue

make: symbol lookup error: /usr/lib/libguile-2.2.so.1: undefined symbol:
GC_move_disappearing_link

Will investigate further.

Vincent

Vincent Delecroix

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Jan 20, 2018, 6:41:52 AM1/20/18
to sage-r...@googlegroups.com, sage-devel
Actually, there is a conflict between my system gc and the one that is
installed by Sage. If I simply
- set gc as an optional pkg
- remove any dependency to gc (that is ecl and libhomfly)
Then I was able to compile.

I opened [#24575] for this issue. Any idea on how to solve it?

Vincent

[#24575] https://trac.sagemath.org/ticket/24575
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