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Sage 9.1 dependency problem

asked 2020-07-21 18:48:44 -0500

powerengineer gravatar image

updated 2020-07-21 19:28:31 -0500

slelievre gravatar image

OS: Linux Mint 20

SageMath: sage-9.1-Ubuntu_18.04-x86_64.tar.bz2

Hello all, I am trying to install sage 9.1, but I get this error after the ./configure

configure: notice: the following SPKGs did not find equivalent system packages: boost cbc freetype gp2c isl libsemigroups pari_elldata pari_galpol pari_nftables pari_seadata perl_cpan_polymake_prereq perl_term_readline_gnu python3
checking for the package system in use... conda
configure: hint: installing the following system packages is recommended and may avoid building some of the above SPKGs from source:
configure:   $ conda install boost-cpp coincbc freetype isl pari-galpol pari-seadata
configure: After installation, re-run configure using:
configure:   $ ./config.status --recheck && ./config.status

After installing those packages:

/opt/SageMath$ conda install -c conda-forge boost-cpp coincbc freetype isl pari-galpol pari-seadata
I still get the same error when I rerun ./configure. I tried running make to see what would happen, and I get this:
***************************************************************
Error building Sage.

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

* package:         python3-3.7.3.p1
  last build time: Jul 21 16:25
  log file:        /opt/SageMath/logs/pkgs/python3-3.7.3.p1.log
  build directory: /opt/SageMath/local/var/tmp/sage/build/python3-3.7.3.p1

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]: *** [Makefile:33: all-start] Error 1
make[1]: Leaving directory '/opt/SageMath'
make: *** [Makefile:13: all] Error 2

I am not sure what is wrong. I installed the dependency packages first as well.

$ sudo apt-get install bc binutils bzip2 ca-certificates cliquer curl eclib-tools fflas-ffpack flintqs g++ g++ gcc gcc gfan gfortran git glpk-utils gmp-ecm lcalc libatomic-ops-dev libboost-dev libbraiding-dev libbz2-dev libcdd-dev libcdd-tools libcliquer-dev libcurl4-openssl-dev libec-dev libecm-dev libffi-dev libflint-arb-dev libflint-dev libfreetype6-dev libgd-dev libgf2x-dev libgivaro-dev libglpk-dev libgmp-dev libgsl-dev libiml-dev liblfunction-dev liblrcalc-dev liblzma-dev libm4rie-dev libmpc-dev libmpfi-dev libmpfr-dev libncurses5-dev libntl-dev libopenblas-dev libpari-dev libpcre3-dev libplanarity-dev libppl-dev libreadline-dev librw-dev libsqlite3-dev libsymmetrica2-dev libz-dev libzmq3-dev m4 make nauty pari-doc pari-elldata pari-galdata pari-galpol pari-gp2c pari-seadata patch perl pkg-config planarity ppl-dev python3 python3-distutils python3.7 r-base-dev r-cran-lattice sqlite3 tachyon tar xz-utils yasm
I could not get libpython3.7-dev to install; the package does not seem available, but i could get the python 3.8 version.

Thank you for all the help

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answered 2020-07-21 22:53:13 -0500

Emmanuel Charpentier gravatar image

The cause of your problems probably pointed to in /opt/SageMath/logs/pkgs/python3-3.7.3.p1.log. It may or may not be related to the presence/absence of system packages ; however, Sage will (should) install a "local" version of missing system packages if necessary.

BTW, you may obtain better answer to questions about sage installation and possible bugs by posting your question to sage-support.

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Thank you very much. I was unaware of the sage-support site.

powerengineer gravatar imagepowerengineer ( 2020-07-23 13:07:12 -0500 )edit

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Asked: 2020-07-21 18:48:44 -0500

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Last updated: Jul 21