Problem compiling SAGE8.4 on debian 9.5

asked 2018-10-30 06:42:24 -0600

anonymous user

Anonymous

updated 2018-11-01 10:25:58 -0600

FrédéricC gravatar image

Problem compiling SAGE8.4 on debian 9.5

Found local metadata for gfan-0.6.2.p0
Using cached file /opt/SAGE/sage-8.4/upstream/gfan0.6.2.tar.gz
gfan-0.6.2.p0
====================================================
Setting up build directory for gfan-0.6.2.p0
Finished extraction
Applying patches from ../patches...
Applying ../patches/Makefile.patch
patching file Makefile
Applying ../patches/maketestsreturnerror.patch
patching file src/app_test.cpp
Applying ../patches/nodel.patch
patching file src/app_main.cpp
Applying ../patches/truncate0008outputs.patch
patching file testsuite/0008PolynomialSetUnion/command
patching file testsuite/0008PolynomialSetUnion/output
patching file testsuite/0008PolynomialSetUnion/outputNew
****************************************************
Host system:
Linux localhost.localdomain 4.9.0-8-amd64 #1 SMP Debian 4.9.110-3+deb9u6 (2018-10-08) x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 6.3.0-18+deb9u1' --with-bugurl=file:///usr/share/doc/gcc-6/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-6 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-6-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-6-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-6-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 6.3.0 20170516 (Debian 6.3.0-18+deb9u1) 
****************************************************
No record that 'gfan' was ever installed; skipping uninstall
Now building gfan...
make[4]: Entering directory '/opt/SAGE/sage-8.4/local/var/tmp/sage/build/gfan-0.6.2.p0/src'
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/polynomialgcd.cpp -o src/polynomialgcd.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/lp_cdd.cpp -o src/lp_cdd.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/parser.cpp -o src/parser.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/field.cpp -o src/field.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/monomial.cpp -o src/monomial.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/printer.cpp -o src/printer.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/polynomial.cpp -o src/polynomial.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/termorder.cpp -o src/termorder.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/term.cpp -o src/term.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/vektor.cpp -o src/vektor.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/division.cpp -o src/division.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/buchberger.cpp -o src/buchberger.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/wallideal.cpp -o src/wallideal.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/lp.cpp -o src/lp.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/enumeration.cpp -o src/enumeration.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/ep_standard.cpp -o src/ep_standard.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/ep_xfig.cpp -o src/ep_xfig.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/reversesearch.cpp -o src/reversesearch.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/application.cpp -o src/application.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/timer.cpp -o src/timer.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/renderer.cpp -o src/renderer.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/field_rationals.cpp -o src/field_rationals.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/symmetry.cpp -o src/symmetry.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/breadthfirstsearch.cpp -o src/breadthfirstsearch.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/genericwalk.cpp -o src/genericwalk.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/minkowskisum.cpp -o src/minkowskisum.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/newtonpolytope.cpp -o src/newtonpolytope.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/tropical.cpp -o src/tropical.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/dimension.cpp -o src/dimension.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/bergman.cpp -o src/bergman.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/subspace.cpp -o src/subspace.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/polyhedralcone.cpp -o src/polyhedralcone.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/gfanapplication.cpp -o src/gfanapplication.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/polyhedralfan.cpp -o src/polyhedralfan.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/tropical2.cpp -o src/tropical2.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/field_zmodpz.cpp -o src/field_zmodpz.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/binomial.cpp -o src/binomial.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/matrix.cpp -o src/matrix.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/latticeideal.cpp -o src/latticeideal.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/scarf.cpp -o src/scarf.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/xfig.cpp -o src/xfig.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/halfopencone.cpp -o src/halfopencone.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/lll.cpp -o src/lll.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/multiplicity.cpp -o src/multiplicity.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/substitute.cpp -o src/substitute.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/polymakefile.cpp -o src/polymakefile.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/saturation.cpp -o src/saturation.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/determinant.cpp -o src/determinant.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/polynomialring.cpp -o src/polynomialring.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/log.cpp -o src/log.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/tropicalbasis.cpp -o src/tropicalbasis.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/symmetriccomplex.cpp -o src/symmetriccomplex.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/linalg.cpp -o src/linalg.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/minors.cpp -o src/minors.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/continuedfractions.cpp -o src/continuedfractions.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/triangulation.cpp -o src/triangulation.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/minkowskidual.cpp -o src/minkowskidual.o
g++  -std=c++11 -DNOCDDPREFIX -DGMPRATIONAL -Wuninitialized -fno-omit-frame-pointer -O2   -g     -c src/regularsubdivision.cpp -o src/regularsubdivision.o
In file included from /usr/include/c++/6/bits/uniform_int_dist.h:35:0,
                 from /usr/include/c++/6/bits/stl_algo.h:66,
                 from /usr/include/c++/6/algorithm:62,
                 from src/matrix.h:7,
                 from src/regularsubdivision.h:5,
                 from src/regularsubdivision.cpp:1:
/usr/include/c++/6/limits:451:12: internal compiler error: Segmentation fault
     struct numeric_limits<char>
            ^~~~~~~~~~~~~~~~~~~~
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-6/README.Bugs> for instructions.
Makefile:505: recipe for target 'src/regularsubdivision.o' failed
make[4]: *** [src/regularsubdivision.o] Error 1
make[4]: Leaving directory '/opt/SAGE/sage-8.4/local/var/tmp/sage/build/gfan-0.6.2.p0/src'
Error building gfan.

real    1m37.513s
user    1m33.320s
sys 0m3.792s
************************************************************************
Error installing package gfan-0.6.2.p0
************************************************************************
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/opt/SAGE/sage-8.4/local/var/tmp/sage/build/gfan-0.6.2.p0 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
  (cd '/opt/SAGE/sage-8.4/local/var/tmp/sage/build/gfan-0.6.2.p0' && '/opt/SAGE/sage-8.4/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************

/0/4                               processor      Intel(R) Core(TM) i5-5200U CPU @ 2.20GHz
/0/25                              memory         16GiB System Memory
/0/1/0.0.0             /dev/sda    disk           500GB Samsung SSD 860

ii  g++                                                              4:6.3.0-4                                   amd64        GNU C++ compiler
ii  g++-6                                                            6.3.0-18+deb9u1                             amd64        GNU C++ compiler
ii  gawk                                                             1:4.1.4+dfsg-1                              amd64        GNU awk, a pattern scanning and processing language
ii  gcc                                                              4:6.3.0-4                                   amd64        GNU C compiler
ii  gcc-6                                                            6.3.0-18+deb9u1                             amd64        GNU C compiler
ii  gcc-6-base:amd64                                                 6.3.0-18+deb9u1                             amd64        GCC, the GNU Compiler Collection (base package)
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Comments

Did you follow http://doc.sagemath.org/html/en/insta... in particular:

  • did you instal the following packages: binutils gcc g++ gfortran make m4 perl tar git openssl libssl-dev
  • which commands did you run ?
tmonteil gravatar imagetmonteil ( 2018-10-30 07:09:57 -0600 )edit