Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
Hi everybody. Got sage running ok this time. % sage ┌┐ │ SageMath version 9.3.beta4, Release Date: 2020-12-14 │ │ Using Python 3.9.1. Type "help()" for help.│ I essentially had to 1) remove my /usr/local, 2) install a fresh brew, 3) install the latest Xcode and Command line, and 4) cleanup my .zshrc This is surprising as for the previous version of sage this worked relatively smoothly. Thanks for all the tips - I have learned a lot. Pierre Le mercredi 16 décembre 2020 à 13:27:19 UTC+1, dim...@gmail.com a écrit : > On Wed, Dec 16, 2020 at 12:15 PM Pierre Vanhove > wrote: > > > > 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. > > This is wrong. > This can only happen if you've set some environment variable used > internally by Sage to some (wrong) values. > > these files belong to /local/bin > and not to $HOME/local/bin > > What is the output of > > set | grep SAGE > > (normally it's just empty, or perhaps has SAGE_CHECK there, but no more) > > Are you by any chance trying to build Sage inside its shell, e.g. > ./sage -sh > or > ./sage -buildsh > > ? > > > > > > > > > > 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 > >> 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 > 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 depende
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
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 > 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 > 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//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 > 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
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
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. 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 > 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//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 > 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 co
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
Hi - so I've tried to recompile (after distclean etc. ) now I get another compilation error Error installing package markupsafe-1.1.1 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 > 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
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
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 >>>>> wrote: >>>>> > >>>>> > hi >>>>> > >>>>> > >>>>> > What did one do yesterday just after 17:00 on the machine? >>>>> > Updated Homebrew? Install
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
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 >>>> 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. >>
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
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 >> 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+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/fe2d8a5e-d5aa-41d4-9508-e0d8712211fcn%40googlegroups.com.
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
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. 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.pie...@gmail.com) | web: http://sites.google.com/site/vanhovepierre/ <https://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+unsubscr...@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.
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
Hi > Do you by any chance try to use Brew's gcc and g++? no as I remember. > What is the output of > > ls -l /usr/local/include/stdio.h % ls -l /usr/local/include/stdio.h lrwxr-xr-x 1 root admin 71 déc 14 17:11 /usr/local/include/stdio.h -> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h This looks like the standard MacOS distrib. I will try conda …. thanks, Pierre > Le 15 déc. 2020 à 13:54, Dima Pasechnik a écrit : > > On Tue, Dec 15, 2020 at 12:47 PM Pierre Vanhove > mailto:vanhove.pie...@gmail.com>> wrote: >> >> no idea ? Should I remove this? I don’t know how this came in. > > This is only a symptom of something going on wrongly. > > Do you by any chance try to use Brew's gcc and g++? > What is the output of > > ls -l /usr/local/include/stdio.h > >> >> Le 15 déc. 2020 à 13:45, Dima Pasechnik a écrit : >> >> You have weird stuff in /usr/local, e.g. what's >> >> /usr/local/include/stdio.h >> >> I see in your log? No wonder it can break things. >> >> >> >> On Tue, Dec 15, 2020 at 12:40 PM Pierre Vanhove >> wrote: >> >> >> hi >> >> Since no compilation was succesfull I tried sage-9.3-beta4. >> >> My homebrew version is >> >> % brew --version >> Homebrew 2.6.2 >> Homebrew/homebrew-core (git revision 9d75f; last commit 2020-12-15) >> Homebrew/homebrew-cask (git revision 152f2; last commit 2020-12-15) >> >> Despite doing >> >> source /Users/pierre/local/sage-9.3.beta4/.homebrew-build-env >> >> then >> >> ./configure --enable-sirocco --enable-jupyterlab_widgets >> >> still does not find the installed package. In particular ntl which fails to >> compile. >> >> What should be done now? >> >> I'm attaching the config.log >> >> thanks, Pierre >> >> Le mardi 15 décembre 2020 à 10:30:36 UTC+1, dim...@gmail.com a écrit : >> >> >> the error is >> >> gcc -bundle -undefined dynamic_lookup -L/usr/local/lib -isysroot >> /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk >> -L/Users/pierre/local/sage-9.2/local/lib >> -Wl,-rpath,/Users/pierre/local/sage-9.2/local/lib >> -Wp,-U_FORTIFY_SOURCE >> build/temp.macosx-10.15-x86_64-3.9/build/src/cysignals/signals.o >> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib >> -L/usr/local/opt/sqlite/lib -o >> build/lib.macosx-10.15-x86_64-3.9/cysignals/signals.cpython-39-darwin.so >> -lpari -pthread >> ld: illegal thread local variable reference to regular symbol >> _PARI_SIGINT_block for architecture x86_64 >> clang: error: linker command failed with exit code 1 (use -v to see >> invocation) >> >> so this is something to do with multi- vs single-threaded Pari, I guess. >> It seems that Pari is built single-threaded, but cysignals does not know it. >> >> >> On Tue, Dec 15, 2020 at 12:02 AM John H Palmieri wrote: >> >> >> Maybe something is going wrong with using the homebrew version of Python — >> some conflict somewhere — so could you try >> >> make distclean >> ./configure --with-system-python3=no >> make >> >> (I'm having different problems with the system python: see my posts about >> MACOSX_DEPLOYMENT_TARGET.) >> >> -- >> John >> >> >> On Monday, December 14, 2020 at 2:07:11 AM UTC-8 vanhove...@gmail.com wrote: >> >> >> Hello, >> >> Sage 9.2 fails to build because of cysignals on macos 10.15.7 >> >> Error installing package cysignals-1.10.2 >> >> I had been able to build Sage 9.2 from source when it came out. >> >> Then I tried to install the optional package sirocco, the -i optional >> failed, so I used -p and tried to rebuild sage from source. Now, I'm getting >> this compilation failure. >> >> What should I do? >> >> Thank you for your help, >> Pierre Vanhove >> >> >> -- >> 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/ec07ba9b-8b4e-4ed9-918a-5b2286b3bd91n%40googlegroups.com. >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-devel" group. >> To unsubscribe from thi
Re: [sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
no idea ? Should I remove this? I don’t know how this came in. > Le 15 déc. 2020 à 13:45, Dima Pasechnik a écrit : > > You have weird stuff in /usr/local, e.g. what's > > /usr/local/include/stdio.h > > I see in your log? No wonder it can break things. > > > > On Tue, Dec 15, 2020 at 12:40 PM Pierre Vanhove > mailto:vanhove.pie...@gmail.com>> wrote: >> >> hi >> >> Since no compilation was succesfull I tried sage-9.3-beta4. >> >> My homebrew version is >> >> % brew --version >> Homebrew 2.6.2 >> Homebrew/homebrew-core (git revision 9d75f; last commit 2020-12-15) >> Homebrew/homebrew-cask (git revision 152f2; last commit 2020-12-15) >> >> Despite doing >> >> source /Users/pierre/local/sage-9.3.beta4/.homebrew-build-env >> >> then >> >> ./configure --enable-sirocco --enable-jupyterlab_widgets >> >> still does not find the installed package. In particular ntl which fails to >> compile. >> >> What should be done now? >> >> I'm attaching the config.log >> >> thanks, Pierre >> >> Le mardi 15 décembre 2020 à 10:30:36 UTC+1, dim...@gmail.com a écrit : >>> >>> the error is >>> >>> gcc -bundle -undefined dynamic_lookup -L/usr/local/lib -isysroot >>> /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk >>> -L/Users/pierre/local/sage-9.2/local/lib >>> -Wl,-rpath,/Users/pierre/local/sage-9.2/local/lib >>> -Wp,-U_FORTIFY_SOURCE >>> build/temp.macosx-10.15-x86_64-3.9/build/src/cysignals/signals.o >>> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib >>> -L/usr/local/opt/sqlite/lib -o >>> build/lib.macosx-10.15-x86_64-3.9/cysignals/signals.cpython-39-darwin.so >>> -lpari -pthread >>> ld: illegal thread local variable reference to regular symbol >>> _PARI_SIGINT_block for architecture x86_64 >>> clang: error: linker command failed with exit code 1 (use -v to see >>> invocation) >>> >>> so this is something to do with multi- vs single-threaded Pari, I guess. >>> It seems that Pari is built single-threaded, but cysignals does not know it. >>> >>> >>> On Tue, Dec 15, 2020 at 12:02 AM John H Palmieri >>> wrote: >>>> >>>> Maybe something is going wrong with using the homebrew version of Python — >>>> some conflict somewhere — so could you try >>>> >>>> make distclean >>>> ./configure --with-system-python3=no >>>> make >>>> >>>> (I'm having different problems with the system python: see my posts about >>>> MACOSX_DEPLOYMENT_TARGET.) >>>> >>>> -- >>>> John >>>> >>>> >>>> On Monday, December 14, 2020 at 2:07:11 AM UTC-8 vanhove...@gmail.com >>>> wrote: >>>>> >>>>> Hello, >>>>> >>>>> Sage 9.2 fails to build because of cysignals on macos 10.15.7 >>>>> >>>>> Error installing package cysignals-1.10.2 >>>>> >>>>> I had been able to build Sage 9.2 from source when it came out. >>>>> >>>>> Then I tried to install the optional package sirocco, the -i optional >>>>> failed, so I used -p and tried to rebuild sage from source. Now, I'm >>>>> getting this compilation failure. >>>>> >>>>> What should I do? >>>>> >>>>> Thank you for your help, >>>>> Pierre Vanhove >>>> >>>> -- >>>> 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/ec07ba9b-8b4e-4ed9-918a-5b2286b3bd91n%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+unsubscr...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-devel/f380bdc2-be50-421b-9600-f37ade174d8fn%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+unsubscr...@googlegroups.com > <mailto:sage-devel+unsubscr...@googlegroups.com>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAAWYfq1%3DE_zgKC1-dz8BA3GrMk07UFncB065E%3DKP4ZCuvPdCHQ%40mail.gmail.com > > <https://groups.google.com/d/msgid/sage-devel/CAAWYfq1%3DE_zgKC1-dz8BA3GrMk07UFncB065E%3DKP4ZCuvPdCHQ%40mail.gmail.com>. Pierre Vanhove (vanhove.pie...@gmail.com) | web: http://sites.google.com/site/vanhovepierre/ <https://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+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/AF3DDC38-B279-4EEC-96DB-30A092E46C80%40gmail.com.
[sage-devel] sage-9.3.beta4 fails to compile
Hi since sage-9.2 fails to recompile from source, I have tried sage-9.3-beta4 sage does not find the homebrew packages $ brew install pandoc ffmpeg imagemagick texinfo arb flint ntl ppl despite having run source .homebrew-build-env which are already installed. My brew version is % brew --version Homebrew 2.6.2 Homebrew/homebrew-core (git revision 9d75f; last commit 2020-12-15) Homebrew/homebrew-cask (git revision 152f2; last commit 2020-12-15) Then sage tried to build ntl which fails [ntl-11.4.3] Error installing package ntl-11.4.3 and compilation fails. How can I get sage back to work on macos 10.15.7 thank you, Pierre Vanhove -- 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+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/7c03388c-dac6-41ea-8df0-5a18cffa12d3n%40googlegroups.com.
[sage-devel] Sage 9.2 fails to build because of cysignals on macos 10.15.7
Hello, Sage 9.2 fails to build because of cysignals on macos 10.15.7 Error installing package cysignals-1.10.2 I had been able to build Sage 9.2 from source when it came out. Then I tried to install the optional package sirocco, the -i optional failed, so I used -p and tried to rebuild sage from source. Now, I'm getting this compilation failure. What should I do? Thank you for your help, Pierre Vanhove -- 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+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/36288985-134c-4887-894d-d64c3b525fafn%40googlegroups.com. Found local metadata for cysignals-1.10.2 Using cached file /Users/pierre/local/sage-9.2/upstream/cysignals-1.10.2.tar.gz cysignals-1.10.2 Setting up build directory for cysignals-1.10.2 Finished extraction No patch files found in ../patches Host system: Darwin macbookpro-vanhove.dyndns.cern.ch 19.6.0 Darwin Kernel Version 19.6.0: Thu Oct 29 22:56:45 PDT 2020; root:xnu-6153.141.2.2~1/RELEASE_X86_64 x86_64 C compiler: gcc C compiler version: Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1 Apple clang version 12.0.0 (clang-1200.0.32.27) Target: x86_64-apple-darwin19.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin Package 'cysignals' is currently not installed No legacy uninstaller found for 'cysignals'; nothing to do Configuring cysignals-1.10.2 configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether gcc accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/local/bin/ggrep checking for egrep... /usr/local/bin/ggrep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking sys/mman.h usability... yes checking sys/mman.h presence... yes checking for sys/mman.h... yes checking sys/prctl.h usability... no checking sys/prctl.h presence... no checking for sys/prctl.h... no checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/wait.h usability... yes checking sys/wait.h presence... yes checking for sys/wait.h... yes checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for fork... yes checking for kill... yes checking for sigprocmask... yes checking for sigaltstack... yes checking for backtrace... yes checking for library containing pari_init... -lpari checking whether PARI_SIGINT_block is declared... yes checking for emms instruction... yes checking whether setjmp() saves the signal mask... yes checking for GNU libc... no checking for _Atomic in C code... yes checking for _Atomic in C++ code... yes checking for std::atomic... yes configure: creating ./config.status config.status: creating src/cysignals/signals.pxd config.status: creating src/config.h config.status: creating src/cysignals/cysignals_config.h configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking Installing cysignals-1.10.2 Ignoring indexes: https://pypi.org/simple Created temporary directory: /private/var/folders/fj/hhdkjbx57yb2kx64bwgym434gq/T/pip-ephem-wheel-cache-szlheziw Created temporary directory: /private/var/folders/fj/hhdkjbx57yb2kx64bwgym434gq/T/pip-req-tracker-usbt5wi4 Initialized build tracking at /private/var/folders/fj/hhdkjbx57yb2kx64bwgym434gq/T/pip-req-tracker-usbt5wi4 Created build tracker: /private/var/folders/fj/hhdkjbx57yb2kx64bwgym434gq/T/pip-req-tracker-usbt5wi4 Entered build tracker: /private/var/folders/fj/hhdkjbx57yb2kx64bwgym434gq/T/pip-req-tracker-usbt5w
