On Fri, 22 Nov 2019 at 01:34, Paul Masson <paulmas...@comcast.net> wrote:
> That did it! Thanks Dima and John. Hope I won't have to build fresh with > every little system package installed. > distclean is certainly an overkill in such cases. Basically, if you replace a package X with a system package, you might need to rebuild all the packages that depend on X, and this should be automatic (but not too robust :() what is not automatic is de-installation of Sage’s package X, and one needs to run make X-clean before running ./configure && make > > On Thursday, November 21, 2019 at 2:45:33 PM UTC-8, John H Palmieri wrote: > >> I have what looks like a very similar setup: `pkg-config --libs libpng` >> returns the same thing, I have symlinks for those two files, but matplotlib >> finds libpng just fine. Did you do 'make distclean' after reinstalling >> libpng and pkg-config? What does "brew list" say? >> >> >> On Thursday, November 21, 2019 at 1:43:05 PM UTC-8, Paul Masson wrote: >>> >>> Both are present as symlinks >>> >>> On Thursday, November 21, 2019 at 1:35:24 PM UTC-8, Dima Pasechnik wrote: >>>> >>>> >>>> >>>> On Thu, 21 Nov 2019, 21:09 Paul Masson, <paulm...@comcast.net> wrote: >>>> >>>>> After installing both libpng and pkg-config, and making sure both are >>>>> completely updated, building Sage still fails on matplotlib with the same >>>>> error. Here is an output requested yesterday: >>>>> >>>>> pkg-config --libs libpng >>>>> >>>>> -L/usr/local/Cellar/libpng/1.6.37/lib -lpng16 -lz >>>>> >>>>> >>>>> I added /usr/local/Cellar to my $PATH. Build still fails for >>>>> matplotlib. >>>>> >>>>> >>>>> Before I ignore the system libpng when building, is there anything >>>>> else I should try? >>>>> >>>> >>>> do you have /usr/local/include/png.h and /usr/local/lib/libpng.dylib >>>> present? >>>> >>>> >>>>> On Wednesday, November 20, 2019 at 4:36:02 PM UTC-8, Dima Pasechnik >>>>> wrote: >>>>>> >>>>>> On Wed, Nov 20, 2019 at 11:56 PM Paul Masson <paulm...@comcast.net> >>>>>> wrote: >>>>>> > >>>>>> > I'd like to understand why this is now necessary. I've been >>>>>> building Sage on this Mac for several years without having this happen. I >>>>>> think the last "make distclean" I did was in April. What might have >>>>>> changed >>>>>> in the meantime? Perhaps this is relevant: >>>>>> https://trac.sagemath.org/ticket/27186 >>>>>> >>>>>> Sure, now a system version of libpng is used by default. >>>>>> We're trying to unvendor as much as possible from Sage the >>>>>> distribution, see >>>>>> https://trac.sagemath.org/ticket/27330 >>>>>> - something which is a necessary step towards make sagelib a "normal" >>>>>> Python library, >>>>>> which you could install by running pip. >>>>>> >>>>>> So, yes, if you have a stale library somewhere it might break the >>>>>> build, as it's not really >>>>>> possible to test on all the possible broken configurations. >>>>>> >>>>>> You may force building of libpng by doing >>>>>> >>>>>> ./configure --without-system-png >>>>>> >>>>>> before running make >>>>>> >>>>>> Hope this explains. >>>>>> > >>>>>> > On Wednesday, November 20, 2019 at 3:38:12 PM UTC-8, Dima Pasechnik >>>>>> wrote: >>>>>> >> >>>>>> >> you can do >>>>>> >> >>>>>> >> brew install libpng >>>>>> >> >>>>>> >> which would install libpng 1.6.37 into /usr/local/ >>>>>> >> (I think, by looking at >>>>>> >> >>>>>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/libpng.rb) >>>>>> >>>>>> >> >>>>>> >> you can also install a lot of other homebrew packages, such as >>>>>> gmp, etc >>>>>> >> to account for more packages on >>>>>> https://trac.sagemath.org/ticket/27330 >>>>>> >> >>>>>> >> >>>>>> >> I've tweaked/wrote some Homebrew formulas to get flint and arb >>>>>> >> >>>>>> >> brew install dimpase/science/flint >>>>>> >> brew install dimpase/science/arb >>>>>> >> >>>>>> >> from https://github.com/dimpase/homebrew-science >>>>>> >> >>>>>> >> (probably many more can be done this way too) >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> On Wed, Nov 20, 2019 at 11:22 PM Paul Masson <paulm...@comcast.net> >>>>>> wrote: >>>>>> >> > >>>>>> >> > I have Homebrew installed but have rarely used it so assumed it >>>>>> wasn't part of the problem. It needed updating, but then the Sage build >>>>>> stopped with the same matplotlib error. >>>>>> >> > >>>>>> >> > libpng-config --cflags >>>>>> >> > >>>>>> >> > -I/usr/local/Cellar/libpng/1.6.34/include/libpng16 >>>>>> >> > >>>>>> >> > >>>>>> >> > libpng-config --ldflags >>>>>> >> > >>>>>> >> > -L/usr/local/Cellar/libpng/1.6.34/lib -lpng16 >>>>>> >> > >>>>>> >> > >>>>>> >> > Guess I'll do a manual install with Homebrew unless there is a >>>>>> better idea. >>>>>> >> > >>>>>> >> > >>>>>> >> > On Wednesday, November 20, 2019 at 2:38:21 PM UTC-8, Dima >>>>>> Pasechnik wrote: >>>>>> >> >> >>>>>> >> >> So you do have old (the current libpng there is 1.6.37, not >>>>>> 1.6.34) >>>>>> >> >> Homebrew (?) installed (or perhaps not 100% de-installed), with >>>>>> libpng >>>>>> >> >> installed in Cellar only (?) for some reason. It causes >>>>>> trouble, as it >>>>>> >> >> is (as well as matplolib's handling >>>>>> >> >> of dependence discovery) is a bit broken. >>>>>> >> >> >>>>>> >> >> more our of curiosity, what are outputs of >>>>>> >> >> >>>>>> >> >> libpng-config --cflags >>>>>> >> >> libpng-config --ldflags >>>>>> >> >> >>>>>> >> >> If you don't need it libpng, you can just remove it. >>>>>> >> >> Else, you can remove it only for the Sage building. >>>>>> >> >> Or you can update your Homebrew, properly install libpng etc... >>>>>> >> >> >>>>>> >> >> >>>>>> >> >> On Wed, Nov 20, 2019 at 10:17 PM Paul Masson < >>>>>> paulm...@comcast.net> wrote: >>>>>> >> >> > >>>>>> >> >> > For the first: >>>>>> >> >> > >>>>>> >> >> > otool -L local/lib/libgd.dylib >>>>>> >> >> > >>>>>> >> >> > local/lib/libgd.dylib: >>>>>> >> >> > >>>>>> >> >> > /Users/Masson/Downloads/GitHub/sage/local/lib/libgd.3.dylib >>>>>> (compatibility version 4.0.0, current version 4.0.0) >>>>>> >> >> > >>>>>> >> >> > /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, >>>>>> current version 7.0.0) >>>>>> >> >> > >>>>>> >> >> > /usr/lib/libz.1.dylib (compatibility version 1.0.0, current >>>>>> version 1.2.11) >>>>>> >> >> > >>>>>> >> >> > >>>>>> /Users/Masson/Downloads/GitHub/sage/local/lib/libfreetype.6.dylib >>>>>> (compatibility version 23.0.0, current version 23.1.0) >>>>>> >> >> > >>>>>> >> >> > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, >>>>>> current version 1281.0.0) >>>>>> >> >> > >>>>>> >> >> > >>>>>> >> >> > And the second: >>>>>> >> >> > >>>>>> >> >> > >>>>>> >> >> > libpng-config --prefix >>>>>> >> >> > >>>>>> >> >> > /usr/local/Cellar/libpng/1.6.34 >>>>>> >> >> > >>>>>> >> >> > >>>>>> >> >> > On Wednesday, November 20, 2019 at 2:12:17 PM UTC-8, Dima >>>>>> Pasechnik wrote: >>>>>> >> >> >> >>>>>> >> >> >> also please post the output of >>>>>> >> >> >> >>>>>> >> >> >> libpng-config --prefix >>>>>> >> >> >> >>>>>> >> >> >> >>>>>> >> >> >> On Wed, Nov 20, 2019 at 10:05 PM Dima Pasechnik < >>>>>> dim...@gmail.com> wrote: >>>>>> >> >> >> > >>>>>> >> >> >> > hmm, strange. So it is found somewhere, not clear where. >>>>>> One way to >>>>>> >> >> >> > see is to check linking of libgd >>>>>> >> >> >> > >>>>>> >> >> >> > otool -L local/lib/libgd.dylib >>>>>> >> >> >> > >>>>>> >> >> >> > or perhaps in >>>>>> >> >> >> > >>>>>> >> >> >> > logs/pkgs/libgd* >>>>>> >> >> >> > >>>>>> >> >> >> > On Wed, Nov 20, 2019 at 9:49 PM Paul Masson < >>>>>> paulm...@comcast.net> wrote: >>>>>> >> >> >> > > >>>>>> >> >> >> > > Here it is >>>>>> >> >> >> > > >>>>>> >> >> >> > > On Wednesday, November 20, 2019 at 1:39:19 PM UTC-8, >>>>>> Dima Pasechnik wrote: >>>>>> >> >> >> > >> >>>>>> >> >> >> > >> please post config.log >>>>>> >> >> >> > >> you have a mysterious copy of libpng somewhere... >>>>>> >> >> >> > >> >>>>>> >> >> >> > >> On Wed, Nov 20, 2019 at 9:36 PM Paul Masson < >>>>>> paulm...@comcast.net> wrote: >>>>>> >> >> >> > >> > >>>>>> >> >> >> > >> > I do not have anaconda installed. Building from the >>>>>> git repository with no package managers. >>>>>> >> >> >> > >> > >>>>>> >> >> >> > >> > On Wednesday, November 20, 2019 at 1:31:10 PM UTC-8, >>>>>> Dima Pasechnik wrote: >>>>>> >> >> >> > >> >> >>>>>> >> >> >> > >> >> Probably anaconda conflict, do you have pkg-config >>>>>> installed, so that >>>>>> >> >> >> > >> >> >>>>>> >> >> >> > >> >> pkg-config --libs libpng >>>>>> >> >> >> > >> >> >>>>>> >> >> >> > >> >> outputs a path to anaconda? >>>>>> >> >> >> > >> >> >>>>>> >> >> >> > >> >> I guess matplotlib does not use pkg-config, so it >>>>>> can't find libpng in >>>>>> >> >> >> > >> >> an unusual location. >>>>>> >> >> >> > >> >> >>>>>> >> >> >> > >> >> On Wed, Nov 20, 2019 at 7:57 PM Paul Masson < >>>>>> paulm...@comcast.net> wrote: >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > On macOS 10.15.1, after "make distclean" I get >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > The following package(s) may have failed to build >>>>>> (not necessarily >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > during this run of 'make all-start'): >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > * package: matplotlib-2.2.4.p0 >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > log file: >>>>>> /Users/Masson/Downloads/GitHub/sage/logs/pkgs/matplotlib-2.2.4.p0.log >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > build directory: >>>>>> /Users/Masson/Downloads/GitHub/sage/local/var/tmp/sage/build/matplotlib-2.2.4.p0 >>>>>> >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > In the attached log, it says that libpng is not >>>>>> installed. I've never seen this error before, but I didn't think I'd have >>>>>> to install anything manually that was mandatory for the build. Thoughts? >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > >>>>>> >> >> >> > >> >> > On Sunday, November 17, 2019 at 4:42:15 PM UTC-8, >>>>>> Volker Braun wrote: >>>>>> >> >> >> > >> >> >> >>>>>> >> >> >> > >> >> >> 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 >>>>>> >> >> >> > >> >> >> >>>>>> >> >> >> > >> >> >> This is the first Python 3 beta, so incremental >>>>>> builds probably aren't going to work. Use "make distclean" or the >>>>>> appropriate configure flag to keep using Python 2 (noooo) >>>>>> >> >> >> > >> >> >> >>>>>> >> >> >> > >> >> >> >>>>>> >> >> >> > >> >> >> 232ae1bddc (tag: 9.0.beta6) Updated SageMath >>>>>> version to 9.0.beta6 >>>>>> >> >> >> > >> >> >> 026a216fa4 Trac #28104: Openblas build failure >>>>>> >> >> >> > >> >> >> 1e7795c1f2 Trac #28726: py3: cysignals fails its >>>>>> test suite >>>>>> >> >> >> > >> >> >> c53e82c055 Trac #28734: a few miscellanous >>>>>> details >>>>>> >> >> >> > >> >> >> a55e518077 Trac #28721: Document >>>>>> sage-dist-helpers >>>>>> >> >> >> > >> >> >> c87212c10b Trac #28715: remove some deprecated >>>>>> stuff in combinat after 23319 and 15597 >>>>>> >> >> >> > >> >> >> 2adaf8bc28 Trac #28686: Demote some optional >>>>>> packages to experimental >>>>>> >> >> >> > >> >> >> 381ddacd15 Trac #15077: Inconsistency in >>>>>> polynomial .reverse(n) >>>>>> >> >> >> > >> >> >> af4d15a8e1 Trac #28725: fix lawrence_extension >>>>>> and lawrence_polytope for backend field >>>>>> >> >> >> > >> >> >> a8e457e711 Trac #28719: remove deprecated >>>>>> function aliases >>>>>> >> >> >> > >> >> >> e46f2a5383 Trac #28717: some cleanup in __init__ >>>>>> files >>>>>> >> >> >> > >> >> >> 9101b22829 Trac #28709: Python executable in >>>>>> doctest/control.py >>>>>> >> >> >> > >> >> >> 6544bf8e40 Trac #28707: More control on the >>>>>> numerical ODE solver for integrated curves and geodesics >>>>>> >> >> >> > >> >> >> 50034a0ae9 Trac #28652: Rework the constructor of >>>>>> PermutationGroupElement >>>>>> >> >> >> > >> >> >> edc1360355 Trac #28606: CombinatorialPolyhedron: >>>>>> unbounded -> is_bounded >>>>>> >> >> >> > >> >> >> 3a35510660 Trac #28605: CombinatorialPolyhedron: >>>>>> replace attributes by methods >>>>>> >> >> >> > >> >> >> 133435b38d Trac #27302: Cubic Braid Groups >>>>>> >> >> >> > >> >> >> 8d41eaeed4 Trac #27089: >>>>>> CPLEXBackend.solver_parameter: Handle CPX_PARAMTYPE_LONG >>>>>> >> >> >> > >> >> >> eb5d0df260 Trac #25183: Bug in the associahedron >>>>>> object >>>>>> >> >> >> > >> >> >> 94b6adde10 Trac #24108: >>>>>> quadratic_form_from_invariants() >>>>>> >> >> >> > >> >> >> e9e14ad864 Trac #28730: cvxopt fails its test >>>>>> suite >>>>>> >> >> >> > >> >> >> a9146cd62b Trac #28714: clarify docstring of >>>>>> plot.colors.float_to_integer >>>>>> >> >> >> > >> >> >> f94189b015 Trac #28708: 5 cplex doctests failed >>>>>> in cplex_backend.pyx >>>>>> >> >> >> > >> >> >> 92a0045e31 Trac #28700: Fixing missing optional >>>>>> flag in base_QQ.py >>>>>> >> >> >> > >> >> >> 6c5f93dfb4 Trac #28689: py3: fix doctests with >>>>>> cbc >>>>>> >> >> >> > >> >> >> 3dd1d44175 Trac #28660: Make Python 3 the default >>>>>> >> >> >> > >> >> >> 0a86718461 Trac #28382: Correct types in cplex >>>>>> backend >>>>>> >> >> >> > >> >> >> 82b36b2ead Trac #27761: DES Block Cipher >>>>>> >> >> >> > >> >> >> 93db4cc438 (tag: 9.0.beta5) Updated SageMath >>>>>> version to 9.0.beta5 >>>>>> >> >> >> > >> >> >> 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