trouble upgrading to latest stable version

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Anne Schilling

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May 25, 2020, 12:40:42 AM5/25/20
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Hi All,

I seem to have trouble upgrading my Sage to the latest stable version:

sage anne$ make
make -j4 build/make/Makefile --stop
./bootstrap -d
rm -rf config configure build/make/Makefile-auto.in
rm -f src/doc/en/installation/*.txt
src/doc/bootstrap:48: installing src/doc/en/installation/arch.txt and src/doc/en/installation/arch-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/debian.txt and src/doc/en/installation/debian-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/fedora.txt and src/doc/en/installation/fedora-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/cygwin.txt and src/doc/en/installation/cygwin-optional.txt
src/doc/bootstrap:48: installing src/doc/en/installation/homebrew.txt and src/doc/en/installation/homebrew-optional.txt
gettext and the gettextize program must be installed and be in
your PATH. E.g. Homebrew installs them in /usr/local/opt/gettext/bin.
Bootstrap failed, downloading required files instead.
Attempting to download package configure-765c5cb3e24dd134708eca97e4c52e0221cd94ba.tar.gz from mirrors
Downloading the Sage mirror list
CRITICAL [mirror_list|_load:91]: Downloaded mirror list has syntax error: error code: 1010
Searching fastest mirror
ERROR [mirror_list|_rank_mirrors:145]: Could not reach any mirror directly and no proxy set
************************************************************************
Traceback (most recent call last):
  File "/Applications/sage/build/bin/../sage_bootstrap/download/cmdline.py", line 130, in run_safe
    run()
  File "/Applications/sage/build/bin/../sage_bootstrap/download/cmdline.py", line 112, in run
    app.download_tarball(args.url_or_tarball, args.destination, args.allow_upstream)
  File "/Applications/sage/build/bin/../sage_bootstrap/download/app.py", line 41, in download_tarball
    tarball.download(allow_upstream=allow_upstream)
  File "/Applications/sage/build/bin/../sage_bootstrap/tarball.py", line 156, in download
    for mirror in MirrorList():
  File "/Applications/sage/build/bin/../sage_bootstrap/download/mirror_list.py", line 69, in __init__
    self._refresh()
  File "/Applications/sage/build/bin/../sage_bootstrap/download/mirror_list.py", line 185, in _refresh
    self._rank_mirrors()
  File "/Applications/sage/build/bin/../sage_bootstrap/download/mirror_list.py", line 146, in _rank_mirrors
    raise MirrorListException('Failed to connect to any mirror, probably no internet connection')
MirrorListException: Failed to connect to any mirror, probably no internet connection
************************************************************************
Error: downloading configure-765c5cb3e24dd134708eca97e4c52e0221cd94ba.tar.gz failed
make[1]: *** [configure] Error 1
make: *** [base-toolchain] Error 2


Any idea why?

Best,

Anne

Matthias Koeppe

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May 25, 2020, 1:27:19 AM5/25/20
to sage-devel
Hi Anne,


On Sunday, May 24, 2020 at 9:40:42 PM UTC-7, Anne Schilling wrote:
Downloading the Sage mirror list
CRITICAL [mirror_list|_load:91]: Downloaded mirror list has syntax error: error code: 1010
Searching fastest mirror
ERROR [mirror_list|_rank_mirrors:145]: Could not reach any mirror directly and no proxy set

Here's a workaround:

echo '["http://files.sagemath.org/"]' > upstream/mirror_list 


I hope this helps,
Matthias

Anne Schilling

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May 25, 2020, 2:44:27 AM5/25/20
to sage-devel
Thank you, that got me a lot further. But now it is stuck here:

[matplotlib-2.2.5]     running install_egg_info
[matplotlib-2.2.5]     running egg_info
[matplotlib-2.2.5]     writing lib/matplotlib.egg-info/PKG-INFO
[matplotlib-2.2.5]     writing dependency_links to lib/matplotlib.egg-info/dependency_links.txt
[matplotlib-2.2.5]     writing namespace_packages to lib/matplotlib.egg-info/namespace_packages.txt
[matplotlib-2.2.5]     writing requirements to lib/matplotlib.egg-info/requires.txt
[matplotlib-2.2.5]     writing top-level names to lib/matplotlib.egg-info/top_level.txt
[matplotlib-2.2.5]     reading manifest file 'lib/matplotlib.egg-info/SOURCES.txt'
[matplotlib-2.2.5]     reading manifest template 'MANIFEST.in'
[matplotlib-2.2.5]     writing manifest file 'lib/matplotlib.egg-info/SOURCES.txt'
[matplotlib-2.2.5]     Copying lib/matplotlib.egg-info to /Applications/sage/local/var/tmp/sage/build/matplotlib-2.2.5/inst/Applications/sage/local/lib/python3.7/site-packages/matplotlib-2.2.5-py3.7.egg-info
[matplotlib-2.2.5]     Installing /Applications/sage/local/var/tmp/sage/build/matplotlib-2.2.5/inst/Applications/sage/local/lib/python3.7/site-packages/matplotlib-2.2.5-py3.7-nspkg.pth
[matplotlib-2.2.5]     running install_scripts
[matplotlib-2.2.5]     writing list of installed files to '/private/var/folders/sq/gx2hlzhj315g48j_8r39s8p80000gp/T/pip-record-rmt5izi9/install-record.txt'
[matplotlib-2.2.5]     Running setup.py install for matplotlib: finished with status 'done'
[matplotlib-2.2.5]   Removing source in /private/var/folders/sq/gx2hlzhj315g48j_8r39s8p80000gp/T/pip-req-build-l19fxrx8
[matplotlib-2.2.5] Successfully installed matplotlib-2.2.5
[matplotlib-2.2.5] Cleaning up...
[matplotlib-2.2.5] Removed build tracker '/private/var/folders/sq/gx2hlzhj315g48j_8r39s8p80000gp/T/pip-req-tracker-rxz0bq3j'
[matplotlib-2.2.5]
[matplotlib-2.2.5] real    6m10.218s
[matplotlib-2.2.5] user    0m35.266s
[matplotlib-2.2.5] sys    0m4.548s
[matplotlib-2.2.5] Copying package files from temporary location /Applications/sage/local/var/tmp/sage/build/matplotlib-2.2.5/inst to /Applications/sage/local
[matplotlib-2.2.5] Successfully installed matplotlib-2.2.5
[matplotlib-2.2.5] Deleting temporary build directory
[matplotlib-2.2.5] /Applications/sage/local/var/tmp/sage/build/matplotlib-2.2.5
[matplotlib-2.2.5] Finished installing matplotlib-2.2.5.spkg
make[2]: *** [all-start] Error 2

real    48m47.186s
user    162m58.074s
sys    27m3.413s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package:         r-3.6.2.p0
  last build time: May 24 23:28
  log file:        /Applications/sage/logs/pkgs/r-3.6.2.p0.log
  build directory: /Applications/sage/local/var/tmp/sage/build/r-3.6.2.p0

* documentation:         dochtml
  last build time: May 24 22:43
  log file:        /Applications/sage/logs/pkgs/../dochtml.log

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: *** [all-start] Error 1
make: *** [all] Error 2

 I can provide the log files if necessary.

Best,

Anne

Furkan Semih Dündar

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May 25, 2020, 3:06:06 AM5/25/20
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Dear Anne,

I tried to compile the source code on Windows Subsystem for Linux (Ubuntu) and could not go through the compilation process. Then I installed Fedora 32 as a separate OS. I installed all the packages listed on the following website: https://doc.sagemath.org/html/en/installation/source.html#prerequisites

Then I let my computer compile the source code at night, when I woke up it was compiled successfully.

Hope this might help.

Best wishes,
Furkan.

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Dima Pasechnik

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May 25, 2020, 4:29:33 AM5/25/20
to sage-devel
Are you building from scratch?
What is your setup? (Sage nowadays supports building with Homebrew packages)

Yes, naturally, without the log files for R and dochtml one cannot say
what went wrong.
Also, the top-level config.log woud be useful.

Best
Dima

Anne Schilling

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May 25, 2020, 12:27:56 PM5/25/20
to sage-devel
Hi Dima,

I pulled the changes using git in the master branch and started make (or make distclean).
This is running on MacOS 10.12.6 .


Thank you!

Anne
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-...@googlegroups.com.

Dima Pasechnik

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May 25, 2020, 1:52:29 PM5/25/20
to sage-devel
Hi Anne,
it appears from your config.log that you did not do 

make distclean

moreover, it says that R is already installed, and should not get reinstalled.

Does Sage start? I guess not.
If before the latest git pull you had an oldish Sage (closer to 9.0 than to 9.1)
it appears that the build system is totally confused.
So you most probably need to do distclean.

HTH
Dima



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Anne Schilling

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May 25, 2020, 7:11:28 PM5/25/20
to sage-devel
Hi Dima,

Thank you! I have run make distclean and now it gets stuck here:


It looks like there is a problem with openssl.

Any idea?

Anne

Dima Pasechnik

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May 25, 2020, 7:37:22 PM5/25/20
to sage-devel
Hi Anne,
openssl is a never-ending problem on macOS, and in your case it's made
worse by an old macOS version.
One cannot expect much support and development on macOS 10.12, as it
has reached EOL in 2019.

One way out would be to install Python 3.7 from cpython, and then Sage
will just use it, without building.

https://www.python.org/ftp/python/3.7.7/python-3.7.7-macosx10.9.pkg

(or, alternatively, install Homebrew, then you can use many more
packages from there without building)

HTH
Dima

On Tue, May 26, 2020 at 12:11 AM Anne Schilling
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Matthias Koeppe

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May 25, 2020, 9:05:42 PM5/25/20
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I agree, updating the OS if possible, and/or installing homebrew and python3 from homebrew would be the way to go.

Anne Schilling

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May 25, 2020, 9:13:46 PM5/25/20
to sage-devel
Thank you! I have homebrew installed. So I just do

brew install python3 ?

Installing the python package that Dima suggested did not help.
I am trying to avoid installing a new operating system right now since I anyway ordered a new computer.

Best,

Anne

Matthias Koeppe

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May 25, 2020, 9:35:01 PM5/25/20
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Could you try with the commands:

 . ./.homebrew-build-env
 ./configure

and post the output of the latter?

Anne Schilling

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May 25, 2020, 9:59:09 PM5/25/20
to sage-devel


On Monday, May 25, 2020 at 6:35:01 PM UTC-7, Matthias Koeppe wrote:
Could you try with the commands:

 . ./.homebrew-build-env
 ./configure

and post the output of the latter?

After installing python3 with homebrew is got further. Now it hangs here:


Here is the output Matthias requested:

. ./.homebrew-build-env
lolita:sage anne$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make -j4 sets $(MAKE)... yes
checking whether make -j4 supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for root user... no
checking build system type... x86_64-apple-darwin16.7.0
checking host system type... x86_64-apple-darwin16.7.0
checking for a sed that does not truncate output... /usr/bin/sed
checking for ar... yes
checking for m4... yes
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ranlib... yes
checking for strip... yes
checking for GNU or BSD tar... /usr/bin/tar
checking for Python... /usr/local/bin/python3
checking for latex... yes
checking for perl... /usr/bin/perl
checking for Perl version 5.8.0 or later... yes
checking whether a conda environment is active... no
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 gcc understands -c and -o together... yes
checking whether make -j4 supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking for gfortran... no
checking for g95... no
checking for xlf95... no
checking for f95... no
checking for fort... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgfortran... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking for nagfor... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking whether we are using the GNU Fortran compiler... no
checking whether  accepts -g... no
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... yes
checking whether gcc accepts -g... yes
checking dependency style of gcc... none
checking for g++... g++
checking whether we are using the GNU Objective C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -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 complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for sqrt in -lm... yes
You are using OS X Lion (or later).
You are strongly advised to install Apple's latest Xcode
unless you already have it. You can install this using
the App Store. Also, make sure you install Xcode's
Command Line Tools -- see Sage's README.txt.
checking Python version to install... 3
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG gcc...
checking for C compiler vendor... clang
checking whether g++ supports C++11 features with -std=gnu++11... yes
checking for gcc option to accept ISO C99... none needed
checking if gcc accepts -dumpversion option... yes
checking gcc version... 4.2.1
checking if g++ accepts -dumpversion option... yes
checking g++ version... 4.2.1
configure: will use system package and not install SPKG gcc
checking for the location of crti.o...
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG mpir...
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
checking gmpxx.h usability... yes
checking gmpxx.h presence... yes
checking for gmpxx.h... yes
checking for library containing __gmpq_cmp_z... -lgmp
configure: will use system package and not install SPKG mpir
checking absolute name of <gmp.h>... checking for gmp.h... (cached) yes
///usr/local/include/gmp.h
using GMP-compatible library from the system
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG gmp...
configure: will use system package and not install SPKG gmp
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG mpfr...
checking installing gmp/mpir? ... no
checking mpfr.h usability... yes
checking mpfr.h presence... yes
checking for mpfr.h... yes
checking for library containing mpfr_free_pool... -lmpfr
configure: will use system package and not install SPKG mpfr
using mpfr library from the system
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG ntl...
checking installing gmp/mpir? ... no
checking NTL/ZZ.h usability... no
checking NTL/ZZ.h presence... no
checking for NTL/ZZ.h... no
checking whether we can link a program using NTL... no
checking NTL version >= 10.3... configure: no suitable system package found for SPKG ntl
using Sage's ntl SPKG
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG flint...
checking installing mpfr or ntl? ... yes; install flint as well
configure: no suitable system package found for SPKG flint
using Sage's flint SPKG
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG arb...
checking installing flint? ... yes; install arb as well
configure: no suitable system package found for SPKG arb
checking for Fortran flag needed to accept free-form source... unknown
configure: Your Fortran compiler does not accept free-format source code
configure: which means the compiler is either seriously broken, or
configure: is too old to build Sage.
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG gfortran...
configure: gfortran has already been installed by SageMath
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG openblas...
checking BLAS library... openblas
checking whether any of gfortran is installed as or will be installed as SPKG... yes; install openblas as well
configure: no suitable system package found for SPKG openblas
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG atlas...
configure: SPKG atlas is not required on this system
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG boost_cropped...
configure: boost_cropped has already been installed by SageMath
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG boost...
checking whether any of boost_cropped is installed as or will be installed as SPKG... yes; install boost as well
configure: no suitable system package found for SPKG boost
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG bzip2...
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for library containing BZ2_bzCompress... -lbz2
checking for bzip2... /usr/bin/bzip2
configure: will use system package and not install SPKG bzip2
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG zlib...
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for LIBPNG... yes
configure: will use system package and not install SPKG zlib
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG cbc...
checking whether any of atlas openblas zlib bzip2 is installed as or will be installed as SPKG... yes; install cbc as well
configure: no suitable system package found for SPKG cbc
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG cddlib...
checking whether any of gmp mpir is installed as or will be installed as SPKG... no
checking for cddexec... no
checking for cddexec_gmp... no
checking for redcheck_gmp... no
checking for scdd_gmp... no
checking for scdd... no
checking for cdd.h... no
checking for library containing dd_abs... no
configure: no suitable system package found for SPKG cddlib
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG cliquer...
checking for library containing clique_unweighted_max_weight... no
configure: no suitable system package found for SPKG cliquer
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG cmake...
checking for cmake >= 3.4...
configure: no suitable system package found for SPKG cmake
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG curl...
checking for curl 7.22... /usr/bin/curl
checking for gawk... (cached) awk
checking for curl-config... /usr/bin/curl-config
checking for the version of libcurl... 7.54.0
checking for libcurl >= version 7.22... yes
checking whether libcurl is usable... yes
checking for curl_free... yes
checking whether programs linking to libcurl can be executed... yes
configure: will use system package and not install SPKG curl
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG ncurses...
checking for NCURSES... no
checking ncurses.h usability... yes
checking ncurses.h presence... yes
checking for ncurses.h... yes
checking for library containing wresize... -lncurses
configure: will use system package and not install SPKG ncurses
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG readline...
checking Installing ncurses? ... No.
checking for READLINE... yes
configure: will use system package and not install SPKG readline
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pari...
checking whether any of gmp mpir readline is installed as or will be installed as SPKG... no
checking for gp... no
configure: gp is not found
configure: no suitable system package found for SPKG pari
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG eclib...
checking whether any of ntl pari flint is installed as or will be installed as SPKG... yes; install eclib as well
configure: no suitable system package found for SPKG eclib
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG ecm...
checking installing gmp/mpir? ... no.
checking ecm.h usability... no
checking ecm.h presence... no
checking for ecm.h... no
configure: no suitable system package found for SPKG ecm
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG givaro...
checking whether any of gmp mpir is installed as or will be installed as SPKG... no
checking for givaro-config... no
configure: givaro-config not found. Installing givaro
configure: no suitable system package found for SPKG givaro
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG fflas_ffpack...
checking whether any of atlas givaro gmp mpir openblas is installed as or will be installed as SPKG... yes; install fflas_ffpack as well
configure: no suitable system package found for SPKG fflas_ffpack
checking whether C++ compiler accepts -mavx512f -mavx512vl -mavx512dq... yes
checking whether C++ compiler accepts -mfma... yes
checking whether C++ compiler accepts -mfma4... yes
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG flintqs...
checking for QuadraticSieve... no
configure: no suitable system package found for SPKG flintqs
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG fplll...
checking whether any of mpfr is installed as or will be installed as SPKG... no
checking for FPLLL... no
configure: no suitable system package found for SPKG fplll
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG libpng...
checking installing zlib? ... no
checking for LIBPNG... yes
configure: will use system package and not install SPKG libpng
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG freetype...
checking Installing libpng? ... no
checking for FREETYPE... yes
configure: will use system package and not install SPKG freetype
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG gf2x...
configure: gf2x has already been installed by SageMath
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG gfan...
checking for gfan >= 0.6.2...
configure: no suitable system package found for SPKG gfan
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG git...
checking for git... /usr/bin/git
configure: will use system package and not install SPKG git
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG glpk...
checking whether any of gmp mpir zlib is installed as or will be installed as SPKG... no
checking for glpsol... no
configure: glpsol not found. Installing glpk
configure: no suitable system package found for SPKG glpk
using Sage's glpk SPKG
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG gp2c...
checking whether any of pari is installed as or will be installed as SPKG... yes; install gp2c as well
configure: no suitable system package found for SPKG gp2c
configure: pari.cfg is $SAGE_LOCAL/lib/pari/pari.cfg
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG gsl...
checking whether any of atlas openblas is installed as or will be installed as SPKG... yes; install gsl as well
configure: no suitable system package found for SPKG gsl
checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking for shared library run path origin... done
checking 32-bit host C ABI... no
checking for the common suffixes of directories in the library search path... lib,lib
checking for iconv... yes
checking for working iconv... yes
checking how to link with libiconv... -liconv
checking for iconv declaration...
         extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG iconv...
configure: will use system package and not install SPKG iconv
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG iml...
checking whether any of gmp mpir openblas is installed as or will be installed as SPKG... yes; install iml as well
configure: no suitable system package found for SPKG iml
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG isl...
checking installing gmp/mpir? ... no
checking for ISL... yes
configure: will use system package and not install SPKG isl
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG lcalc...
checking whether any of pari mpfr is installed as or will be installed as SPKG... yes; install lcalc as well
configure: no suitable system package found for SPKG lcalc
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG libatomic_ops...
checking for LIBATOMIC_OPS... no
configure: no suitable system package found for SPKG libatomic_ops
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG libbraiding...
checking if we can link against libbraiding... no
configure: no suitable system package found for SPKG libbraiding
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG libffi...
checking for LIBFFI... yes
configure: will use system package and not install SPKG libffi
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG libgd...
checking Installing freetype? ... checking Installing libpng? ... No.
checking for LIBGD... no
configure: no suitable system package found for SPKG libgd
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG libsemigroups...
checking for LIBSEMIGROUPS... no
configure: no suitable system package found for SPKG libsemigroups
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG lrcalc...
checking for lrcalc/schublib.h... no
configure: no suitable system package found for SPKG lrcalc
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG m4ri...
checking whether any of libpng is installed as or will be installed as SPKG... no
checking for M4RI... no
configure: no suitable system package found for SPKG m4ri
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG m4rie...
checking whether any of m4ri is installed as or will be installed as SPKG... yes; install m4rie as well
configure: no suitable system package found for SPKG m4rie
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG mpc...
checking installing mpfr? ... no
checking mpc.h usability... yes
checking mpc.h presence... yes
checking for mpc.h... yes
checking for library containing mpc_cmp_abs... -lmpc
configure: will use system package and not install SPKG mpc
using mpc library from the system
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG mpfi...
checking installing mpfr? ... no
checking mpfi.h usability... no
checking mpfi.h presence... no
checking for mpfi.h... no
checking for library containing mpfi_diam_abs... no
configure: no suitable system package found for SPKG mpfi
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG nauty...
checking for geng... no
checking for nauty-geng... no
configure: no suitable system package found for SPKG nauty
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG ninja_build...
checking for ninja >= 1.7.2...
configure: no suitable system package found for SPKG ninja_build
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pandoc...
checking for pandoc... /usr/local/bin/pandoc
configure: will use system package and not install SPKG pandoc
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pari_elldata...
checking installing pari? ... yes; install pari_elldata as well
configure: no suitable system package found for SPKG pari_elldata
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pari_galdata...
checking installing pari? ... yes; install pari_galdata as well
configure: no suitable system package found for SPKG pari_galdata
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pari_galpol...
checking installing pari? ... yes; install pari_galpol as well
configure: no suitable system package found for SPKG pari_galpol
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pari_nftables...
checking installing pari? ... yes; install pari_nftables as well
configure: no suitable system package found for SPKG pari_nftables
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pari_seadata_small...
checking installing pari? ... yes; install pari_seadata_small as well
configure: no suitable system package found for SPKG pari_seadata_small
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pari_seadata...
checking installing pari? ... yes; install pari_seadata as well
configure: no suitable system package found for SPKG pari_seadata
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG patch...
configure: patch has already been installed by SageMath
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pcre...
checking installing bzip2? ... no
checking for PCRE... no
checking pcre.h usability... no
checking pcre.h presence... no
checking for pcre.h... no
checking pcrecpp.h usability... no
checking pcrecpp.h presence... no
checking for pcrecpp.h... no
checking pcreposix.h usability... no
checking pcreposix.h presence... no
checking for pcreposix.h... no
configure: no suitable system package found for SPKG pcre
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG perl_cpan_polymake_prereq...
checking for perl module XML::Writer... ok
checking for perl module XML::LibXML... ok
checking for perl module XML::LibXSLT... ok
checking for perl module File::Slurp... ok
checking for perl module JSON... no
checking for perl module SVG... no
checking for perl module MongoDB... no
configure: no suitable system package found for SPKG perl_cpan_polymake_prereq
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG perl_term_readline_gnu...
checking for perl module Term::ReadLine... ok
checking Term::ReadLine module...... non-GNU
configure: no suitable system package found for SPKG perl_term_readline_gnu
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG pkgconf...
checking for pkg-config >= 0.29... /usr/local/bin/pkg-config
using pkg-config from the system
configure: will use system package and not install SPKG pkgconf
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG planarity...
checking planarity/planarity.h usability... no
checking planarity/planarity.h presence... no
checking for planarity/planarity.h... no
configure: no suitable system package found for SPKG planarity
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG ppl...
checking whether any of glpk gmp mpir is installed as or will be installed as SPKG... yes; install ppl as well
configure: no suitable system package found for SPKG ppl
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG sqlite...
checking libsqlite3 >= sqlite3_min_version... yes
configure: will use system package and not install SPKG sqlite
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG xz...
checking for lzma_raw_decoder in -llzma... yes
checking lzma.h usability... yes
checking lzma.h presence... yes
checking for lzma.h... yes
checking for xz >= 5.0.0... /usr/local/bin/xz
configure: will use system package and not install SPKG xz
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG python3...
checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG... no
checking for python3 >= 3.7.3, < 3.8 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core...
checking ... whether /usr/local/bin/python3.7 is good... yes
checking for python3 >= 3.7.3, < 3.8 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core... /usr/local/bin/python3.7
configure: will use system package and not install SPKG python3
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG r...
checking whether any of atlas openblas iconv readline bzip2 xz pcre curl is installed as or will be installed as SPKG... yes; install r as well
configure: no suitable system package found for SPKG r
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG rw...
checking rw.h usability... no
checking rw.h presence... no
checking for rw.h... no
checking for library containing calculate_level... no
configure: no suitable system package found for SPKG rw
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG symmetrica...
checking symmetrica/def.h usability... no
checking symmetrica/def.h presence... no
checking for symmetrica/def.h... no
configure: no suitable system package found for SPKG symmetrica
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG tachyon...
checking for tachyon... no
configure: tachyon not found. Installing tachyon
configure: no suitable system package found for SPKG tachyon
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG yasm...
checking for yasm supporting the adox instruction... no
configure: no suitable system package found for SPKG yasm
-----------------------------------------------------------------------------
Checking whether SageMath should install SPKG zeromq...
checking zmq.h usability... no
checking zmq.h presence... no
checking for zmq.h... no
configure: WARNING: no valid ZMQ installation was found
configure: no suitable system package found for SPKG zeromq
## ----------------------------------------------------------------------- ##
## Build status for each package:                                          ##
## ----------------------------------------------------------------------- ##
4ti2-1.6.7.p0:                               does not support check for system package; optional, use "./configure --enable-4ti2" to install
alabaster-0.7.12:                            does not support check for system package; will be installed as an SPKG
appnope-0.1.0.p0:                            does not support check for system package; will be installed as an SPKG
arb-2.16.0.p0:                               no suitable system package; will be installed as an SPKG
atlas-3.10.2.p3:                             not required on your platform; SPKG will not be installed
autotools-20141105.p0:                       does not support check for system package; experimental, use "./configure --enable-autotools" to install
awali-1.0.2-190218:                          does not support check for system package; experimental, use "./configure --enable-awali" to install
babel-2.6.0:                                 does not support check for system package; will be installed as an SPKG
backports_abc-0.5:                           does not support check for system package; will be installed as an SPKG
backports_functools_lru_cache-1.5:           does not support check for system package; will be installed as an SPKG
backports_shutil_get_terminal_size-1.0.0.p1: does not support check for system package; will be installed as an SPKG
backports_ssl_match_hostname-3.5.0.1.p0:     does not support check for system package; will be installed as an SPKG
barvinok-0.41.1:                             does not support check for system package; optional, use "./configure --enable-barvinok" to install
beautifulsoup4-none:                         does not support check for system package; optional pip package; use "./sage -i beautifulsoup4" to install
benzene-20130630:                            does not support check for system package; optional, use "./configure --enable-benzene" to install
biopython-none:                              does not support check for system package; optional pip package; use "./sage -i biopython" to install
bleach-3.1.0:                                does not support check for system package; will be installed as an SPKG
bliss-0.73+debian-1+sage-2016-08-02.p0:      does not support check for system package; optional, use "./configure --enable-bliss" to install
boost-1_66_0:                                no suitable system package; optional, use "./configure --enable-boost" to install
boost_cropped-1.66.0.p0:                     already installed as an SPKG
brial-1.2.5:                                 does not support check for system package; will be installed as an SPKG
buckygen-1.1:                                does not support check for system package; optional, use "./configure --enable-buckygen" to install
bzip2-1.0.6-20150304.p0:                     using system package; SPKG will not be installed
cbc-2.9.4.p0:                                no suitable system package; optional, use "./configure --enable-cbc" to install
ccache-3.3.4:                                does not support check for system package; optional, use "./configure --enable-ccache" to install
cddlib-0.94j:                                no suitable system package; will be installed as an SPKG
certifi-2019.3.9:                            does not support check for system package; will be installed as an SPKG
cliquer-1.21.p4:                             no suitable system package; will be installed as an SPKG
cmake-3.11.0:                                no suitable system package; optional, use "./configure --enable-cmake" to install
cocoalib-0.99564:                            does not support check for system package; experimental, use "./configure --enable-cocoalib" to install
combinatorial_designs-20140630.p0:           does not support check for system package; will be installed as an SPKG
compilerwrapper-1.2:                         does not support check for system package; experimental, use "./configure --enable-compilerwrapper" to install
configparser-3.7.4:                          does not support check for system package; will be installed as an SPKG
configure-765c5cb3e24dd134708eca97e4c52e0221cd94ba:does not support check for system package; came preinstalled with the SageMath tarball
conway_polynomials-0.5:                      does not support check for system package; will be installed as an SPKG
coxeter3-8ac9c71723c8ca57a836d6381aed125261e44e9e.p0:does not support check for system package; optional, use "./configure --enable-coxeter3" to install
cryptominisat-5.6.8:                         does not support check for system package; optional, use "./configure --enable-cryptominisat" to install
csdp-6.2.p0:                                 does not support check for system package; optional, use "./configure --enable-csdp" to install
curl-7.62.0.p0:                              using system package; SPKG will not be installed
cvxopt-1.2.3:                                does not support check for system package; will be installed as an SPKG
cycler-0.10.0.p0:                            does not support check for system package; will be installed as an SPKG
cypari-2.1.1:                                does not support check for system package; will be installed as an SPKG
cysignals-1.10.2:                            does not support check for system package; will be installed as an SPKG
cython-0.29.12.p0:                           does not support check for system package; will be installed as an SPKG
d3js-3.4.8:                                  does not support check for system package; optional, use "./configure --enable-d3js" to install
database_cremona_ellcurve-20190911:          does not support check for system package; optional, use "./configure --enable-database_cremona_ellcurve" to install
database_jones_numfield-4:                   does not support check for system package; optional, use "./configure --enable-database_jones_numfield" to install
database_kohel-20160724:                     does not support check for system package; optional, use "./configure --enable-database_kohel" to install
database_mutation_class-1.0:                 does not support check for system package; optional, use "./configure --enable-database_mutation_class" to install
database_odlyzko_zeta-20061209:              does not support check for system package; optional, use "./configure --enable-database_odlyzko_zeta" to install
database_stein_watkins-20110713:             does not support check for system package; optional, use "./configure --enable-database_stein_watkins" to install
database_stein_watkins_mini-20070827:        does not support check for system package; optional, use "./configure --enable-database_stein_watkins_mini" to install
database_symbolic_data-20070206:             does not support check for system package; optional, use "./configure --enable-database_symbolic_data" to install
dateutil-2.8.1:                              does not support check for system package; will be installed as an SPKG
decorator-4.4.0:                             does not support check for system package; will be installed as an SPKG
deformation-d05941b.p0:                      does not support check for system package; optional, use "./configure --enable-deformation" to install
defusedxml-0.6.0:                            does not support check for system package; will be installed as an SPKG
docutils-0.14:                               does not support check for system package; will be installed as an SPKG
dot2tex-2.11.3.p0:                           does not support check for system package; optional, use "./configure --enable-dot2tex" to install
e_antic-0.1.5:                               does not support check for system package; optional, use "./configure --enable-e_antic" to install
ecl-16.1.2.p5:                               does not support check for system package; will be installed as an SPKG
eclib-20190909:                              no suitable system package; will be installed as an SPKG
ecm-7.0.4.p1:                                no suitable system package; will be installed as an SPKG
elliptic_curves-0.8.1:                       does not support check for system package; will be installed as an SPKG
entrypoints-0.3:                             does not support check for system package; will be installed as an SPKG
enum34-1.1.6:                                does not support check for system package; will be installed as an SPKG
fflas_ffpack-2.4.3:                          no suitable system package; will be installed as an SPKG
flask-0.10.1.p0:                             does not support check for system package; optional, use "./configure --enable-flask" to install
flask_autoindex-0.6.p0:                      does not support check for system package; optional, use "./configure --enable-flask_autoindex" to install
flask_babel-0.9.p0:                          does not support check for system package; optional, use "./configure --enable-flask_babel" to install
flask_oldsessions-0.10.p0:                   does not support check for system package; optional, use "./configure --enable-flask_oldsessions" to install
flask_openid-1.2.5.p0:                       does not support check for system package; optional, use "./configure --enable-flask_openid" to install
flask_silk-0.2.p0:                           does not support check for system package; optional, use "./configure --enable-flask_silk" to install
flint-2.5.2.p5:                              no suitable system package; will be installed as an SPKG
flintqs-1.0.p0:                              no suitable system package; will be installed as an SPKG
fplll-5.3.2:                                 no suitable system package; will be installed as an SPKG
fpylll-0.5.1dev:                             does not support check for system package; will be installed as an SPKG
freetype-2.10.1:                             using system package; SPKG will not be installed
fricas-1.3.5:                                does not support check for system package; optional, use "./configure --enable-fricas" to install
frobby-0.9.0.p2:                             does not support check for system package; optional, use "./configure --enable-frobby" to install
functools32-3.2.3-2.p0:                      does not support check for system package; will be installed as an SPKG
future-0.17.1:                               does not support check for system package; will be installed as an SPKG
gambit-15.1.1.p0:                            does not support check for system package; experimental, use "./configure --enable-gambit" to install
gap-4.10.2.p1:                               does not support check for system package; will be installed as an SPKG
gap3-04jul17:                                does not support check for system package; experimental, use "./configure --enable-gap3" to install
gap_jupyter-0.9:                             does not support check for system package; optional, use "./configure --enable-gap_jupyter" to install
gap_packages-4.10.2.p1:                      does not support check for system package; optional, use "./configure --enable-gap_packages" to install
gc-8.0.4:                                    does not support check for system package; will be installed as an SPKG
gcc-9.2.0:                                   using system package; SPKG will not be installed
gdb-8.2:                                     does not support check for system package; experimental, use "./configure --enable-gdb" to install
gf2x-1.2.p0:                                 already installed as an SPKG
gfan-0.6.2.p1:                               no suitable system package; will be installed as an SPKG
gfortran-9.2.0:                              already installed as an SPKG
giac-1.5.0.63-p0:                            does not support check for system package; will be installed as an SPKG
giacpy_sage-0.6.8:                           does not support check for system package; optional, use "./configure --enable-giacpy_sage" to install
git-2.11.0:                                  using system package; SPKG will not be installed
git_trac-20160625.p0:                        does not support check for system package; optional, use "./configure --enable-git_trac" to install
givaro-4.1.1:                                no suitable system package; will be installed as an SPKG
glpk-4.65.p0:                                no suitable system package; will be installed as an SPKG
glucose-4.1:                                 does not support check for system package; optional, use "./configure --enable-glucose" to install
gmp-6.1.2:                                   using system package; SPKG will not be installed
gmpy2-2.1.0b1:                               does not support check for system package; will be installed as an SPKG
gp2c-0.0.10.p0:                              no suitable system package; optional, use "./configure --enable-gp2c" to install
graphs-20161026.p0:                          does not support check for system package; will be installed as an SPKG
gsl-2.5:                                     no suitable system package; will be installed as an SPKG
html5lib-1.0.1:                              does not support check for system package; will be installed as an SPKG
iconv-1.15:                                  using system package; SPKG will not be installed
igraph-0.7.1999.p0:                          does not support check for system package; optional, use "./configure --enable-igraph" to install
imagesize-1.1.0:                             does not support check for system package; will be installed as an SPKG
iml-1.0.4p1.p2:                              no suitable system package; will be installed as an SPKG
ipaddress-1.0.22:                            does not support check for system package; will be installed as an SPKG
ipykernel-4.8.2:                             does not support check for system package; will be installed as an SPKG
ipython-5.8.0:                               does not support check for system package; will be installed as an SPKG
ipython_genutils-0.2.0:                      does not support check for system package; will be installed as an SPKG
ipywidgets-7.4.2:                            does not support check for system package; will be installed as an SPKG
isl-0.20:                                    using system package; SPKG will not be installed
itsdangerous-1.1.0:                          does not support check for system package; will be installed as an SPKG
jinja2-2.10:                                 does not support check for system package; will be installed as an SPKG
jmol-14.29.52:                               does not support check for system package; will be installed as an SPKG
jsonschema-2.6.0:                            does not support check for system package; will be installed as an SPKG
jupymake-0.9:                                does not support check for system package; optional, use "./configure --enable-jupymake" to install
jupyter_client-5.2.4:                        does not support check for system package; will be installed as an SPKG
jupyter_core-4.4.0:                          does not support check for system package; will be installed as an SPKG
kenzo-1.1.7-r3:                              does not support check for system package; optional, use "./configure --enable-kenzo" to install
kiwisolver-1.0.1:                            does not support check for system package; will be installed as an SPKG
latte_int-1.7.5.p0:                          does not support check for system package; optional, use "./configure --enable-latte_int" to install
lcalc-1.23.p19:                              no suitable system package; will be installed as an SPKG
libatomic_ops-7.6.10:                        no suitable system package; will be installed as an SPKG
libbraiding-1.0.p0:                          no suitable system package; will be installed as an SPKG
libffi-3.2.1:                                using system package; SPKG will not be installed
libgd-2.1.1.1.p1:                            no suitable system package; will be installed as an SPKG
libhomfly-1.02r4.p0:                         does not support check for system package; will be installed as an SPKG
libogg-1.3.1.p0:                             does not support check for system package; optional, use "./configure --enable-libogg" to install
libpng-1.6.29.p1:                            using system package; SPKG will not be installed
libsemigroups-0.6.7:                         no suitable system package; optional, use "./configure --enable-libsemigroups" to install
libtheora-1.1.1:                             does not support check for system package; experimental, use "./configure --enable-libtheora" to install
lidia-2.3.0+latte-patches-2019-05-02:        does not support check for system package; optional, use "./configure --enable-lidia" to install
lie-2.2.2:                                   does not support check for system package; experimental, use "./configure --enable-lie" to install
linbox-1.6.3.p0:                             does not support check for system package; will be installed as an SPKG
lrcalc-1.2.p1:                               no suitable system package; will be installed as an SPKG
lrslib-062+autotools-2017-03-03.p1:          does not support check for system package; optional, use "./configure --enable-lrslib" to install
m4ri-20200115:                               no suitable system package; will be installed as an SPKG
m4rie-20200115:                              no suitable system package; will be installed as an SPKG
markupsafe-1.1.0:                            does not support check for system package; will be installed as an SPKG
mathjax-2.7.4.p0:                            does not support check for system package; will be installed as an SPKG
matplotlib-2.2.5:                            does not support check for system package; will be installed as an SPKG
maxima-5.42.2:                               does not support check for system package; will be installed as an SPKG
mcqd-1.0.p0:                                 does not support check for system package; optional, use "./configure --enable-mcqd" to install
meataxe-1.0.p0:                              does not support check for system package; optional, use "./configure --enable-meataxe" to install
mistune-0.8.4:                               does not support check for system package; will be installed as an SPKG
modular_decomposition-20100607:              does not support check for system package; experimental, use "./configure --enable-modular_decomposition" to install
mpc-1.1.0:                                   using system package; SPKG will not be installed
mpfi-1.5.2:                                  no suitable system package; will be installed as an SPKG
mpfr-4.0.1.p0:                               using system package; SPKG will not be installed
mpfrcx-0.5:                                  does not support check for system package; optional, use "./configure --enable-mpfrcx" to install
mpir-3.0.0-644faf502c56f97d9accd301965fc57d6ec70868.p0:using system package; SPKG will not be installed
mpmath-1.1.0:                                does not support check for system package; will be installed as an SPKG
nauty-26r1.p0:                               no suitable system package; will be installed as an SPKG
nbconvert-5.4.0:                             does not support check for system package; will be installed as an SPKG
nbformat-4.4.0:                              does not support check for system package; will be installed as an SPKG
ncurses-6.0.p0:                              using system package; SPKG will not be installed
networkx-2.2:                                does not support check for system package; will be installed as an SPKG
nibabel-none:                                does not support check for system package; optional pip package; use "./sage -i nibabel" to install
ninja_build-1.8.2:                           no suitable system package; optional, use "./configure --enable-ninja_build" to install
normaliz-3.7.2:                              does not support check for system package; optional, use "./configure --enable-normaliz" to install
nose-1.3.7:                                  does not support check for system package; will be installed as an SPKG
notebook-5.7.6.p0:                           does not support check for system package; will be installed as an SPKG
notedown-1.5.1:                              does not support check for system package; optional, use "./configure --enable-notedown" to install
ntl-11.4.3:                                  no suitable system package; will be installed as an SPKG
numpy-1.16.6:                                does not support check for system package; will be installed as an SPKG
openblas-0.3.9:                              no suitable system package; will be installed as an SPKG
openssl-1.1.1g:                              does not support check for system package; optional, use "./configure --enable-openssl" to install
p_group_cohomology-3.3:                      does not support check for system package; optional, use "./configure --enable-p_group_cohomology" to install
packaging-18.0:                              does not support check for system package; will be installed as an SPKG
palp-2.1.p2:                                 does not support check for system package; will be installed as an SPKG
pandoc-none:                                 using system package; SPKG will not be installed
pandoc_attributes-8bc82f6d:                  does not support check for system package; optional, use "./configure --enable-pandoc_attributes" to install
pandocfilters-1.4.2:                         does not support check for system package; will be installed as an SPKG
pari-2.11.2:                                 no suitable system package; will be installed as an SPKG
pari_elldata-20161017:                       no suitable system package; optional, use "./configure --enable-pari_elldata" to install
pari_galdata-20080411.p0:                    no suitable system package; will be installed as an SPKG
pari_galpol-20180625:                        no suitable system package; optional, use "./configure --enable-pari_galpol" to install
pari_jupyter-1.3.2:                          does not support check for system package; optional, use "./configure --enable-pari_jupyter" to install
pari_nftables-20080929:                      no suitable system package; optional, use "./configure --enable-pari_nftables" to install
pari_seadata-20090618:                       no suitable system package; optional, use "./configure --enable-pari_seadata" to install
pari_seadata_small-20090618.p0:              no suitable system package; will be installed as an SPKG
patch-2.7.5:                                 already installed as an SPKG
pathlib2-2.3.3:                              does not support check for system package; will be installed as an SPKG
pathpy-7.1.p0:                               does not support check for system package; will be installed as an SPKG
pcre-8.40.p2:                                no suitable system package; will be installed as an SPKG
perl_cpan_polymake_prereq-none:              no suitable system package; optional, use "./configure --enable-perl_cpan_polymake_prereq" to install
perl_term_readline_gnu-1.35:                 no suitable system package; experimental, use "./configure --enable-perl_term_readline_gnu" to install
pexpect-4.6.0.p0:                            does not support check for system package; will be installed as an SPKG
pickleshare-0.7.5:                           does not support check for system package; will be installed as an SPKG
pillow-5.3.0.p0:                             does not support check for system package; will be installed as an SPKG
pip-18.1:                                    does not support check for system package; will be installed as an SPKG
pkgconf-0.9.7.p2:                            using system package; SPKG will not be installed
pkgconfig-1.5.1:                             does not support check for system package; will be installed as an SPKG
planarity-3.0.0.5.p0:                        no suitable system package; will be installed as an SPKG
plantri-4.5:                                 does not support check for system package; optional, use "./configure --enable-plantri" to install
polylib-5.22.5:                              does not support check for system package; optional, use "./configure --enable-polylib" to install
polymake-3.4:                                does not support check for system package; experimental, use "./configure --enable-polymake" to install
polytopes_db-20170220.p0:                    does not support check for system package; will be installed as an SPKG
ppl-1.2.p1:                                  no suitable system package; will be installed as an SPKG
pplpy-0.8.4:                                 does not support check for system package; will be installed as an SPKG
primecount-5.1:                              does not support check for system package; optional, use "./configure --enable-primecount" to install
prometheus_client-0.5.0:                     does not support check for system package; will be installed as an SPKG
prompt_toolkit-1.0.15:                       does not support check for system package; will be installed as an SPKG
psutil-5.2.0.p2:                             does not support check for system package; will be installed as an SPKG
ptyprocess-0.5.1.p0:                         does not support check for system package; will be installed as an SPKG
pybtex-none:                                 does not support check for system package; optional pip package; use "./sage -i pybtex" to install
pycosat-0.6.3:                               does not support check for system package; optional, use "./configure --enable-pycosat" to install
pycygwin-0.1:                                does not support check for system package; will be installed as an SPKG
pyflakes-none:                               does not support check for system package; optional pip package; use "./sage -i pyflakes" to install
pygments-2.3.1.p0:                           does not support check for system package; will be installed as an SPKG
pynac-0.7.26.sage-2020-04-03:                does not support check for system package; will be installed as an SPKG
pynormaliz-2.7:                              does not support check for system package; optional, use "./configure --enable-pynormaliz" to install
pyopenssl-none:                              does not support check for system package; optional pip package; use "./sage -i pyopenssl" to install
pyparsing-2.3.0:                             does not support check for system package; will be installed as an SPKG
pysingular-0.9.5:                            does not support check for system package; optional, use "./configure --enable-pysingular" to install
python2-2.7.15.p1:                           does not support check for system package; optional, use "./configure --enable-python2" to install
python3-3.7.3.p1:                            using system package; SPKG will not be installed
python_igraph-0.7.1999:                      does not support check for system package; optional, use "./configure --enable-python_igraph" to install
python_openid-2.2.5.p0:                      does not support check for system package; optional, use "./configure --enable-python_openid" to install
pytz-2018.7:                                 does not support check for system package; will be installed as an SPKG
pyx-none:                                    does not support check for system package; optional pip package; use "./sage -i pyx" to install
pyzmq-19.0.0:                                does not support check for system package; will be installed as an SPKG
qepcad-B.1.72:                               does not support check for system package; experimental, use "./configure --enable-qepcad" to install
qhull-2015-src-7.2.0.p1:                     does not support check for system package; optional, use "./configure --enable-qhull" to install
r-3.6.2.p0:                                  no suitable system package; will be installed as an SPKG
r_jupyter-none:                              does not support check for system package; optional, use "./configure --enable-r_jupyter" to install
ratpoints-2.1.3.p5:                          does not support check for system package; will be installed as an SPKG
readline-6.3.008.p0:                         using system package; SPKG will not be installed
requests-2.13.0:                             does not support check for system package; will be installed as an SPKG
rpy2-2.8.2.p1:                               does not support check for system package; will be installed as an SPKG
rst2ipynb-0.2.2.p0:                          does not support check for system package; optional, use "./configure --enable-rst2ipynb" to install
rubiks-20070912.p21:                         does not support check for system package; will be installed as an SPKG
rw-0.7.p0:                                   no suitable system package; will be installed as an SPKG
saclib-2.2.7:                                does not support check for system package; optional, use "./configure --enable-saclib" to install
sage_brial-1.2.5:                            does not support check for system package; will be installed as an SPKG
sage_conf-none:                              does not support check for system package; will be installed as an SPKG
sage_numerical_backends_coin-9.0b12:         does not support check for system package; optional, use "./configure --enable-sage_numerical_backends_coin" to install
sage_numerical_backends_cplex-9.0b12:        does not support check for system package; optional, use "./configure --enable-sage_numerical_backends_cplex" to install
sage_numerical_backends_gurobi-9.0.0:        does not support check for system package; optional, use "./configure --enable-sage_numerical_backends_gurobi" to install
sagenb-1.1.3:                                does not support check for system package; optional, use "./configure --enable-sagenb" to install
sagenb_export-3.3:                           does not support check for system package; will be installed as an SPKG
sagetex-3.4:                                 does not support check for system package; will be installed as an SPKG
scandir-1.9.0:                               does not support check for system package; will be installed as an SPKG
scipoptsuite-5.0.1:                          does not support check for system package; experimental, use "./configure --enable-scipoptsuite" to install
scipy-1.2.3:                                 does not support check for system package; will be installed as an SPKG
scons-1.2.0:                                 does not support check for system package; experimental, use "./configure --enable-scons" to install
send2trash-1.5.0:                            does not support check for system package; will be installed as an SPKG
setuptools-40.6.3:                           does not support check for system package; will be installed as an SPKG
setuptools_scm-3.1.0:                        does not support check for system package; will be installed as an SPKG
simplegeneric-0.8.1.p0:                      does not support check for system package; will be installed as an SPKG
singledispatch-3.4.0.3.p0:                   does not support check for system package; will be installed as an SPKG
singular-4.1.1p2.p0:                         does not support check for system package; will be installed as an SPKG
singular_jupyter-0.9.7:                      does not support check for system package; optional, use "./configure --enable-singular_jupyter" to install
sip-4.18:                                    does not support check for system package; optional, use "./configure --enable-sip" to install
sirocco-2.0.2:                               does not support check for system package; optional, use "./configure --enable-sirocco" to install
six-1.12.0:                                  does not support check for system package; will be installed as an SPKG
snowballstemmer-1.2.1.p0:                    does not support check for system package; will be installed as an SPKG
speaklater-1.3.p0:                           does not support check for system package; optional, use "./configure --enable-speaklater" to install
sphinx-1.8.5.p0:                             does not support check for system package; will be installed as an SPKG
sphinxcontrib_websupport-1.1.0:              does not support check for system package; will be installed as an SPKG
sqlalchemy-none:                             does not support check for system package; optional pip package; use "./sage -i sqlalchemy" to install
sqlite-3290000:                              using system package; SPKG will not be installed
subprocess32-3.5.3:                          does not support check for system package; will be installed as an SPKG
suitesparse-5.6.0:                           does not support check for system package; will be installed as an SPKG
surf-1.0.6-gcc6:                             does not support check for system package; experimental, use "./configure --enable-surf" to install
symmetrica-2.0.p11:                          no suitable system package; will be installed as an SPKG
sympow-1.018.1.p13:                          does not support check for system package; will be installed as an SPKG
sympy-1.5:                                   does not support check for system package; will be installed as an SPKG
tachyon-0.98.9.p7:                           no suitable system package; will be installed as an SPKG
tdlib-0.3.1.p0:                              does not support check for system package; optional, use "./configure --enable-tdlib" to install
termcap-1.3.1.p3:                            does not support check for system package; optional, use "./configure --enable-termcap" to install
terminado-0.8.1:                             does not support check for system package; will be installed as an SPKG
testpath-0.4.2:                              does not support check for system package; will be installed as an SPKG
texlive-none:                                does not support check for system package; optional, use "./configure --enable-texlive" to install
thebe-9624e0a0.p0:                           does not support check for system package; will be installed as an SPKG
threejs-r110:                                does not support check for system package; will be installed as an SPKG
tides-2.0.p0:                                does not support check for system package; optional, use "./configure --enable-tides" to install
topcom-0.17.7:                               does not support check for system package; optional, use "./configure --enable-topcom" to install
tornado-4.5.2:                               does not support check for system package; will be installed as an SPKG
traitlets-4.3.3:                             does not support check for system package; will be installed as an SPKG
twisted-16.3.0.p0:                           does not support check for system package; optional, use "./configure --enable-twisted" to install
typing-3.6.6:                                does not support check for system package; will be installed as an SPKG
valgrind-3.14.0:                             does not support check for system package; experimental, use "./configure --enable-valgrind" to install
vcversioner-2.16.0.0.p0:                     does not support check for system package; will be installed as an SPKG
wcwidth-0.1.7.p0:                            does not support check for system package; will be installed as an SPKG
webencodings-0.5.1:                          does not support check for system package; will be installed as an SPKG
werkzeug-0.14.1:                             does not support check for system package; will be installed as an SPKG
widgetsnbextension-3.4.2:                    does not support check for system package; will be installed as an SPKG
xz-5.2.2.p0:                                 using system package; SPKG will not be installed
yasm-1.3.0.p0:                               no suitable system package; will be installed as an SPKG
zeromq-4.2.5:                                no suitable system package; will be installed as an SPKG
zlib-1.2.11.p0:                              using system package; SPKG will not be installed
zn_poly-0.9.1.p0:                            does not support check for system package; will be installed as an SPKG
zope_interface-4.6.0:                        does not support check for system package; will be installed as an SPKG
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating build/make/Makefile-auto
config.status: creating build/make/Makefile
config.status: creating src/Makefile
config.status: creating src/bin/sage-env-config
config.status: creating build/bin/sage-build-env-config
config.status: creating build/pkgs/sage_conf/src/sage_conf.py
config.status: creating build/pkgs/sage_conf/src/setup.cfg
config.status: executing depfiles commands
config.status: executing mkdirs commands
config.status: creating directory /Applications/sage/logs/pkgs
config.status: creating directory local
config.status: creating directory local/bin
config.status: creating directory local/etc
config.status: creating directory local/include
config.status: creating directory local/lib
config.status: creating directory local/lib/pkgconfig
config.status: creating directory local/share
config.status: creating directory local/var/lib/sage/installed
configure: notice: the following SPKGs did not find equivalent system packages: arb boost cbc cddlib cliquer cmake eclib ecm fflas_ffpack flint flintqs fplll gfan givaro glpk gp2c gsl iml lcalc libatomic_ops libbraiding libgd libsemigroups lrcalc m4ri m4rie mpfi nauty ninja_build ntl openblas pari pari_elldata pari_galdata pari_galpol pari_nftables pari_seadata pari_seadata_small pcre perl_cpan_polymake_prereq perl_term_readline_gnu planarity ppl r rw symmetrica tachyon yasm zeromq
checking for the package system in use... homebrew
configure: hint: installing the following system packages is recommended and may avoid building some of the above SPKGs from source:
configure:   $ brew install boost cmake glpk gsl gd mpfi ninja openblas pcre ppl r yasm zeromq
# To automatically take care of homebrew messages regarding
# keg-only packages for the current shell session:
  $ source /Applications/sage/.homebrew-build-env
# Add this to your shell profile if you want it to persist between shell sessions.
configure: After installation, re-run configure using:
configure:   $ ./config.status --recheck && ./config.status

Matthias Koeppe

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May 25, 2020, 10:41:13 PM5/25/20
to sage-devel
On Monday, May 25, 2020 at 6:59:09 PM UTC-7, Anne Schilling wrote:


On Monday, May 25, 2020 at 6:35:01 PM UTC-7, Matthias Koeppe wrote:
Could you try with the commands:

 . ./.homebrew-build-env
 ./configure

and post the output of the latter?

After installing python3 with homebrew is got further. Now it hangs here:



Looks like there's some really old stuff in /usr/local, perhaps from an ancient homebrew or MacPorts installation?. From the log:


libtool: link: gcc -dynamiclib  -o .libs/libm4ri-0.0.20200115.dylib  m4ri/.libs/brilliantrussian.o m4ri/.libs/misc.o m4ri/.libs/mzd.o m4ri/.libs/graycode.o m4ri/.libs/strassen.o m4ri/.libs/mzp.o m4ri/.libs/triangular.o m4ri/.libs/triangular_russian.o m4ri/.libs/ple.o m4ri/.libs/ple_russian.o m4ri/.libs/solve.o m4ri/.libs/echelonform.o m4ri/.libs/mmc.o m4ri/.libs/debug_dump.o m4ri/.libs/io.o m4ri/.libs/djb.o m4ri/.libs/mp.o   -L/Applications/sage/local/lib -L/usr/local/lib -lpng12 -lz  -mmmx -msse -msse2 -msse3 -g -O2 -Wl,-rpath -Wl,/Applications/sage/local/lib   -install_name  /Applications/sage/local/lib/libm4ri-0.0.20200115.dylib  -Wl,-single_module
ld: warning: ignoring file /usr/local/lib/libpng12.dylib, missing required architecture x86_64 in file /usr/local/lib/libpng12.dylib (2 slices)
Undefined symbols for architecture x86_64:
  "_png_create_info_struct", referenced from:




 

Matthias Koeppe

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May 25, 2020, 10:44:16 PM5/25/20
to sage-devel
You could try if "brew install libpng" fixes this problem (otherwise you'd need to manually clean out /usr/local/lib/libpng*)

Also, note that at the end of the configure output, some commands were recommended: "brew install boost cmake glpk gsl gd mpfi ninja openblas pcre ppl r yasm zeromq"; I second this recommendation 

Anne Schilling

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May 26, 2020, 2:53:50 AM5/26/20
to sage-devel
Thank you! I installed all those. Now it hangs here:


I tried to install freetype by hand, but it does not seem to help.

Matthias Koeppe

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May 26, 2020, 3:00:46 AM5/26/20
to sage-devel
config.log again please...

Anne Schilling

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May 26, 2020, 3:06:57 AM5/26/20
to sage-devel

Matthias Koeppe

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May 26, 2020, 3:11:38 AM5/26/20
to sage-devel
By "install freetype by hand", do you mean you installed with homebrew? 
If not, that's worth trying.
Alternatively, you could try "./configure --without-system-freetype" before "make".

Matthias

Dima Pasechnik

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May 26, 2020, 3:39:37 AM5/26/20
to sage-devel
On Tue, May 26, 2020 at 8:06 AM Anne Schilling
<anne1.s...@gmail.com> wrote:
>
> https://www.math.ucdavis.edu/~anne/config.log

looks like indeed an old libpng in /usr/local breaks things.

(typcally it comes from an ancient installation of TeX).

I would wipe /usr/local (or move it somewhere, for later inspection)
and reinstall Homebrew, then try again.
> --
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Dima Pasechnik

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May 26, 2020, 5:17:49 AM5/26/20
to sage-devel
perhaps before recommending Homebrew, I should have checked that they
fully support 10.13+, and only support 10.11 and 10.12 on
"best-effort" basis.

That is we might be just seeing that their best effort could be
better, and not Sage's bugs :-(

Anne Schilling

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May 26, 2020, 2:24:01 PM5/26/20
to sage-devel
Ok, success!!! Finally sage compiled for me using Matthias' suggestion of "./configure --without-system-freetype"
before make.

Something else must have changed though since sage does not like my sage.init file any longer:

sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.1, Release Date: 2020-05-20                     │
│ Using Python 3.7.7. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
  File "<ipython-input-1-4500cf3fb705>", line 15
    latex_options = {'format': "dot2tex", 'edge_labels':True,'color_by_label':{Integer(1):"blue", Integer(2):"red", Integer(3):"green", Integer(4):"yellow",-Integer(1):"blue", -Integer(2):"red", -Integer(3):"green",-Integer(4):"yellow"}, 'edge_options': lambda (u,v,l): {'backward': l is not None and l>Integer(0)}}
                                                                                                                                                                                                                                                                     ^
SyntaxError: invalid syntax

VulK

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May 26, 2020, 2:59:26 PM5/26/20
to sage-...@googlegroups.com
Unpacking of lambda functions' arguments is, alas, no longer supported in
python3.

cf. https://www.python.org/dev/peps/pep-3113/

S.



* Anne Schilling <anne1.s...@gmail.com> [2020-05-26 11:24:01]:
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Anne Schilling

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May 26, 2020, 4:25:29 PM5/26/20
to sage-devel
Thank you!

Anne
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