no - brew doctor was clean. Now it gives me this
% brew doctor Please note that these warnings are just used to help the Homebrew maintainers with debugging if you file an issue. If everything you use Homebrew for is working fine: please don't worry or file an issue; just ignore this. Thanks! Warning: "config" scripts exist outside your system or Homebrew directories. `./configure` scripts often look for *-config scripts to determine if software packages are installed, and which additional flags to use when compiling and linking. Having additional scripts in your path can confuse software installed via Homebrew if the config script overrides a system or Homebrew-provided script of the same name. We found the following "config" scripts: /Users/pierre/local/bin/givaro-config /Users/pierre/local/bin/fflas-ffpack-config /Users/pierre/local/bin/linbox-config /Users/pierre/local/bin/ecl-config these files are produced by sage compilation. Le mercredi 16 décembre 2020 à 12:15:49 UTC+1, dim...@gmail.com a écrit : > On Wed, Dec 16, 2020 at 10:27 AM Pierre Vanhove > <vanhove...@gmail.com> wrote: > > > > Hi > > >You seem to be trying with the same semi-broken Command Line Tools as > > >we discussed yesterday. > > >Could you please consider installing the latest XCode? > > > > I have done this and my version of Xcode is Version 12.3 (12C33) > > and > > % xcode-select -v > > xcode-select version 2373. > > > > Have you ungraded Homebrew and run > > brew doctor > > afterwards? > > ? I suspect you still have that dodgy headers in /usr/local/include > that we discussed yesterday. > > (check out the top level config.log for this) > > > > Now, compilation just fails at > > > > [setuptools_scm-4.1.2] Error installing package setuptools_scm-4.1.2 > > > > Pierre > > Le mercredi 16 décembre 2020 à 10:51:19 UTC+1, dim...@gmail.com a écrit > : > >> > >> On Wed, Dec 16, 2020 at 9:34 AM Pierre Vanhove <vanhove...@gmail.com> > wrote: > >> > > >> > Hi - so I've tried to recompile (after distclean etc. ) now I get > another compilation error > >> > > >> > Error installing package markupsafe-1.1.1 > >> > >> You seem to be trying with the same semi-broken Command Line Tools as > >> we discussed yesterday. > >> Could you please consider installing the latest XCode? > >> > >> these errors get weirder and weirder. > >> > >> Package 'markupsafe' is currently not installed > >> No legacy uninstaller found for 'markupsafe'; nothing to do > >> Installing markupsafe-1.1.1 > >> Error: Tried to use Sage's Python which was not yet installed. > >> If this was called from an spkg-install script for another > >> package you should add $(PYTHON) as a dependency in > >> build/pkgs/<pkg>/dependencies > >> Error: could not determine package name > >> > >> It says in effect that you need to add $(PYTHON) to > >> build/pkgs/markupsafe/dependencies > >> > >> - but it is already there as far as I can see. > >> > >> > >> > >> > > >> > > >> > Le mercredi 16 décembre 2020 à 10:01:26 UTC+1, dim...@gmail.com a > écrit : > >> >> > >> >> It is not usual that the 1st run went ok, but the next one crashed > on startup. > >> >> Could you try to move away ~/.sage/ and see if it helps? > >> >> (it tends to accumulate incompatible stuff and during updates cause > >> >> all sorts of issues) > >> >> > >> >> If it doesn't help: > >> >> > >> >> Could you provide the output of > >> >> > >> >> otool -L /Users/pierre/local/lib/libSingular-4.1.1.dylib > >> >> > >> >> On Wed, Dec 16, 2020 at 8:22 AM Pierre Vanhove <vanhove...@gmail.com> > wrote: > >> >> > > >> >> > Here is the crash report > >> >> > > >> >> > > >> >> > > >> >> > Le mercredi 16 décembre 2020 à 09:17:14 UTC+1, Pierre Vanhove a > écrit : > >> >> >> > >> >> >> Hi > >> >> >> > >> >> >> thanks for the tips. So I have recompiled sage successfully > >> >> >> > >> >> >> touch > "/Users/pierre/local/sage-9.3.beta4/local/var/lib/sage/installed/sagelib-9.3.beta4" > >> >> >> "/Users/pierre/local/sage-9.3.beta4/build/bin/sage-starts" > >> >> >> > >> >> >> Testing that Sage starts... > >> >> >> [2020-12-16 01:46:39] SageMath version 9.3.beta4, Release Date: > 2020-12-14 > >> >> >> This looks like the first time you are running Sage. > >> >> >> Cleaning up, do not interrupt this. > >> >> >> Done cleaning. > >> >> >> Yes, Sage starts. > >> >> >> > >> >> >> In a terminal window, I started sage. Did 1+1 test. I quit sage, > and launch it again, and sage crashes > >> >> >> > >> >> >> ImportError: > dlopen(/Users/pierre/local/lib/python3.9/site-packages/sage/matrix/ > matrix_mpolynomial_dense.cpython-39-darwin.so, 2): Library not loaded: > /Users/pierre/local/lib/libSingular-4.1.1.dylib > >> >> >> Referenced from: > /Users/pierre/local/lib/python3.9/site-packages/sage/matrix/ > matrix_mpolynomial_dense.cpython-39-darwin.so > >> >> >> Reason: image not found > >> >> >> > >> >> >> I'm sending a crash report. > >> >> >> > >> >> >> Pierre > >> >> >> > >> >> >> > >> >> >> Le mardi 15 décembre 2020 à 21:31:23 UTC+1, zsc...@gmail.com a > écrit : > >> >> >>> > >> >> >>> You can safely ignore that message. I think there is some > ongoing work being done on changing how sage handles recommended packages > and that message is a byproduct. If it's really bothering you then you can > just type: > >> >> >>> > >> >> >>> make _recommended > >> >> >>> > >> >> >>> and I think that message should disappear. > >> >> >>> > >> >> >>> On Tuesday, December 15, 2020 at 3:24:12 PM UTC-5 > vanhove...@gmail.com wrote: > >> >> >>>> > >> >> >>>> hi > >> >> >>>> > >> >> >>>> I have cleanup my /usr/local - reinstalled a fresh brew and > Xcode. > >> >> >>>> I have run ./configure in sage-9.3-beta4 that complained about > missing homebrew package. I have installed them. > >> >> >>>> % brew list > >> >> >>>> aom fribidi harfbuzz libheif little-cms2 pandoc srt > >> >> >>>> arb gcc icu4c libidn2 lzo pcre suite-sparse > >> >> >>>> bdw-gc gd igraph liblqr metis pcre2 tbb > >> >> >>>> boost gdbm ilmbase libmpc mpfi pixman tesseract > >> >> >>>> c-ares gettext imagemagick libogg mpfr pkg-config texinfo > >> >> >>>> cairo ghostscript isl libomp nauty ppl theora > >> >> >>>> cmake giflib jemalloc libpng nettle python@3.9 tox > >> >> >>>> coreutils glib jpeg libsamplerate nghttp2 r unbound > >> >> >>>> dav1d glpk lame libsndfile ninja rav1e webp > >> >> >>>> docbook gmp leptonica libsoxr ntl readline x264 > >> >> >>>> docbook-xsl gnu-getopt libass libtasn1 openblas rtmpdump x265 > >> >> >>>> ffmpeg gnutls libatomic_ops libtiff opencore-amr rubberband > xmlto > >> >> >>>> flac gobject-introspection libbluray libtool openexr sdl2 xvid > >> >> >>>> flint gpatch libde265 libunistring openjpeg shared-mime-info xz > >> >> >>>> fontconfig graphite2 libev libvidstab openssl@1.1 snappy zeromq > >> >> >>>> freetype gsl libevent libvorbis opus speex > >> >> >>>> frei0r guile libffi libvpx p11-kit sqlite > >> >> >>>> > >> >> >>>> my homebrew setup is clean > >> >> >>>> > >> >> >>>> % brew doctor > >> >> >>>> Your system is ready to brew. > >> >> >>>> > >> >> >>>> then boostrapping, sourcing brew environnement and rerun > configure in sage, I still get the message > >> >> >>>> > >> >> >>>> $ brew install pandoc ffmpeg imagemagick texinfo > >> >> >>>> > >> >> >>>> > >> >> >>>> Pierre > >> >> >>>> > >> >> >>>> Le mardi 15 décembre 2020 à 19:57:40 UTC+1, zsc...@gmail.com a > écrit : > >> >> >>>>> > >> >> >>>>> Have you tried running "brew doctor"? Homebrew should complain > loudly about all of the header files in /usr/local/include which could > cause conflicts. For example, if I touch stdio.h in my /usr/local/include > and then I run brew doctor I get: > >> >> >>>>> > >> >> >>>>> "Warning: Unbrewed header files were found in > /usr/local/include. > >> >> >>>>> If you didn't put them there on purpose they could cause > problems when > >> >> >>>>> building Homebrew formulae, and may need to be deleted. > >> >> >>>>> > >> >> >>>>> Unexpected header files: > >> >> >>>>> /usr/local/include/stdio.h" > >> >> >>>>> > >> >> >>>>> I would start with running brew doctor and trying to fix the > recommendations there. > >> >> >>>>> > >> >> >>>>> On Tuesday, December 15, 2020 at 8:43:28 AM UTC-5 > dim...@gmail.com wrote: > >> >> >>>>>> > >> >> >>>>>> On Tue, Dec 15, 2020 at 1:23 PM Pierre Vanhove < > vanhove...@gmail.com> wrote: > >> >> >>>>>> > > >> >> >>>>>> > hi > >> >> >>>>>> > > >> >> >>>>>> > > >> >> >>>>>> > What did one do yesterday just after 17:00 on the machine? > >> >> >>>>>> > Updated Homebrew? Installed macOS command line tools? > >> >> >>>>>> > > >> >> >>>>>> > > >> >> >>>>>> > yes I updated homebrew, but with a bad internet connection > and the connection broke. I had to redo it. > >> >> >>>>>> > > >> >> >>>>>> > But curiously, I have deleted the sage-9.2 folder > downloaded a sage-9.3-beta4 and then worked from the new folder. > >> >> >>>>>> > > >> >> >>>>>> > I will see if using the backup from my time machine solves > the problem by going back in time. > >> >> >>>>>> > >> >> >>>>>> I'd suggest to install the full XCode. The fact that homebrew > >> >> >>>>>> apparently created that link indicates > >> >> >>>>>> that not all is well; I'd also erase the whole /usr/local and > >> >> >>>>>> reinstall Homebrew from scratch, > >> >> >>>>>> after XCode is installed. > >> >> >>>>>> > >> >> >>>>>> macOS, Homebrew, XCode are moving targets, it's hard to keep > up with them. > >> >> >>>>>> > >> >> >>>>>> > > >> >> >>>>>> > Now that they have put sirocco on cocacl, I will work with > that. And I will leave most of the sage coding to Andrey Novoseltsev then > since locally I cannot work... > >> >> >>>>>> > > >> >> >>>>>> > best, Pierre > >> >> >>>>>> > > >> >> >>>>>> > ======================================================== > >> >> >>>>>> > Pierre Vanhove (vanhove...@gmail.com) | web: > http://sites.google.com/site/vanhovepierre/ > >> >> >>>>>> > > >> >> >>>>>> > > >> >> >>>>>> > > >> >> >>>>>> > > >> >> >>>>>> > > >> >> >>>>>> > > >> >> >>>>>> > -- > >> >> >>>>>> > You received this message because you are subscribed to the > Google Groups "sage-devel" group. > >> >> >>>>>> > To unsubscribe from this group and stop receiving emails > from it, send an email to sage-devel+...@googlegroups.com. > >> >> >>>>>> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/95B792F4-B444-4DBB-8E4B-2846A020C683%40gmail.com > . > >> >> > > >> >> > -- > >> >> > You received this message because you are subscribed to the Google > Groups "sage-devel" group. > >> >> > To unsubscribe from this group and stop receiving emails from it, > send an email to sage-devel+...@googlegroups.com. > >> >> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/f8466fc7-c21d-457e-8204-03c9ddc9fcd4n%40googlegroups.com > . > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > Groups "sage-devel" group. > >> > To unsubscribe from this group and stop receiving emails from it, > send an email to sage-devel+...@googlegroups.com. > >> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/2286952c-9ffb-4f68-9b60-9487fd7275cbn%40googlegroups.com > . > > > > -- > > You received this message because you are subscribed to the Google > Groups "sage-devel" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to sage-devel+...@googlegroups.com. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/7381f769-dc73-46f0-9fbf-a57091267298n%40googlegroups.com > . > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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