That did it! Thanks Dima and John. Hope I won't have to build fresh with every little system package installed.
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 >>>>> >> >> >> > >> >> >> >>>>> >> >> >> > >> >> > -- >>>>> >> >> >> > >> >> > You received this message because you 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