On Tue, Sep 10, 2019 at 2:16 PM Mariel Supina
<mariel_sup...@berkeley.edu> wrote:
>
> Hi,
>
> On Tuesday, September 10, 2019 at 2:51:27 PM UTC+2, Dima Pasechnik wrote:
>>
>> On Tue, Sep 10, 2019 at 1:36 PM Mariel Supina
>> <mariel...@berkeley.edu> wrote:
>> >
>> > On Debian stretch, I get a compilation error making sage 8.9.beta9. The 
>> > problem is in the package "cypari", the relevant log is attached:
>>
>> Are you upgrading? Building from scratch?
>
>
> I am building from scratch with python3.
>

could you post the output of ./configure --with-python=3 ?
(I guess that's what you ran before starting to build)

In case you don't know how,  run
./configure --with-python=3 >/tmp/foo

and post the resulting /tmp/foo file

Thanks.

I suspect you have a broken in a interesting way system-wide
installation of pari/gp...

---------------

you can build and use Sage's pari e.g. by
doing

make pari

and then doing

make




>>
>>
>> The interesting line is
>>
>> error: [Errno 2] No such file or directory: '/usr/share/pari/pari.desc'
>>
>> This appears to be related to
>> https://trac.sagemath.org/ticket/28242
>> Perhaps it ought to be improved.
>
>
> The compilation used to work fine on the machines, so that could be it?
>
>>
>>
>> It looks like you're trying to use a system installation of Pari/GP, rather
>> than build Sage's Pari. What parts of Pari (Pari-related packages?)
>> do you have on your Debian system?
>
>
> The computer on which I try to compile is maintained by my department's IT, 
> so I am not completely aware of all the packages that might or might not be 
> installed.
>
> How can I figure out which pari (and which packages) are installed?
>
>>
>>
>> Anyhow, Pari in Stretch is too old, but you should be able to use the
>> one from backports:
>>
>> https://packages.debian.org/stretch-backports/libpari-dev
>
>
> I am afraid that I do not have the rights to install libpari systemwide. Hmm.
>
>>
>>
>>
>> Thanks
>> Dima
>> >
>> > Found local metadata for cypari-2.1.1
>> > Attempting to download package cypari2-2.1.1.tar.gz from mirrors
>> > https://mirror.koddos.net/sagemath/spkg/upstream/cypari/cypari2-2.1.1.tar.gz
>> > [......................................................................]
>> > cypari-2.1.1
>> > ====================================================
>> > Setting up build directory for cypari-2.1.1
>> > Finished extraction
>> > Applying patches from ../patches...
>> > Applying ../patches/trashcan.patch
>> > patching file cypari2/gen.pxd
>> > patching file cypari2/gen.pyx
>> > Hunk #1 succeeded at 141 (offset 6 lines).
>> > patching file cypari2/pari_instance.pyx
>> > ****************************************************
>> > Host system:
>> > Linux ural 4.9.0-9-amd64 #1 SMP Debian 4.9.168-1+deb9u4 (2019-07-19) 
>> > 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)
>> > ****************************************************
>> > Package 'cypari' is currently not installed
>> > No legacy uninstaller found for 'cypari'; nothing to do
>> > Installing cypari-2.1.1
>> > Installing package cypari2 using pip2
>> > Ignoring indexes: https://pypi.org/simple
>> > Created temporary directory: /tmp/pip-ephem-wheel-cache-EMVpJz
>> > Created temporary directory: /tmp/pip-req-tracker-wfmzIV
>> > Created requirements tracker '/tmp/pip-req-tracker-wfmzIV'
>> > Created temporary directory: /tmp/pip-install-HkyCL2
>> > Processing 
>> > /srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src
>> >   Created temporary directory: /tmp/pip-req-build-MoH_HZ
>> >   Added 
>> > file:///srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src 
>> > to build tracker '/tmp/pip-req-tracker-wfmzIV'
>> >   Running setup.py (path:/tmp/pip-req-build-MoH_HZ/setup.py) egg_info for 
>> > package from 
>> > file:///srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src
>> >     Running command python setup.py egg_info
>> >     running egg_info
>> >     creating pip-egg-info/cypari2.egg-info
>> >     writing requirements to pip-egg-info/cypari2.egg-info/requires.txt
>> >     writing pip-egg-info/cypari2.egg-info/PKG-INFO
>> >     writing top-level names to pip-egg-info/cypari2.egg-info/top_level.txt
>> >     writing dependency_links to 
>> > pip-egg-info/cypari2.egg-info/dependency_links.txt
>> >     writing manifest file 'pip-egg-info/cypari2.egg-info/SOURCES.txt'
>> >     error: [Errno 2] No such file or directory: '/usr/share/pari/pari.desc'
>> > Cleaning up...
>> >   Removing source in /tmp/pip-req-build-MoH_HZ
>> > Removed 
>> > file:///srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src 
>> > from build tracker '/tmp/pip-req-tracker-wfmzIV'
>> > Removed build tracker '/tmp/pip-req-tracker-wfmzIV'
>> > Command "python setup.py egg_info" failed with error code 1 in 
>> > /tmp/pip-req-build-MoH_HZ/
>> > Exception information:
>> > Traceback (most recent call last):
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py",
>> >  line 143, in main
>> >     status = self.run(options, args)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/commands/install.py",
>> >  line 318, in run
>> >     resolver.resolve(requirement_set)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
>> >  line 102, in resolve
>> >     self._resolve_one(requirement_set, req)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
>> >  line 256, in _resolve_one
>> >     abstract_dist = self._get_abstract_dist_for(req_to_install)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
>> >  line 209, in _get_abstract_dist_for
>> >     self.require_hashes
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
>> >  line 298, in prepare_linked_requirement
>> >     abstract_dist.prep_for_dist(finder, self.build_isolation)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
>> >  line 126, in prep_for_dist
>> >     self.req.run_egg_info()
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py",
>> >  line 473, in run_egg_info
>> >     command_desc='python setup.py egg_info')
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py",
>> >  line 705, in call_subprocess
>> >     % (command_desc, proc.returncode, cwd))
>> > InstallationError: Command "python setup.py egg_info" failed with error 
>> > code 1 in /tmp/pip-req-build-MoH_HZ/
>> > Error: installing with pip2 failed
>> > ********************************************************************************
>> > Error installing cypari-2.1.1
>> > ********************************************************************************
>> >
>> > real    0m1.345s
>> > user    0m1.088s
>> > sys    0m0.184s
>> > ************************************************************************
>> > Error installing package cypari-2.1.1
>> > ************************************************************************
>> > Please email sage-devel (http://groups.google.com/group/sage-devel)
>> > explaining the problem and including the log file
>> >   /srv/public/shared/sage/logs/pkgs/cypari-2.1.1.log
>> > Describe your computer, operating system, etc.
>> > If you want to try to fix the problem yourself, *don't* just cd to
>> > /srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1 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 '/srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1' && 
>> > '/srv/public/shared/sage/sage' --sh)
>> > When you are done debugging, you can type "exit" to leave the subshell.
>> > ************************************************************************
>> > Found local metadata for cypari-2.1.1
>> > Using cached file /srv/public/shared/sage/upstream/cypari2-2.1.1.tar.gz
>> > cypari-2.1.1
>> > ====================================================
>> > Setting up build directory for cypari-2.1.1
>> > Finished extraction
>> > Applying patches from ../patches...
>> > Applying ../patches/trashcan.patch
>> > patching file cypari2/gen.pxd
>> > patching file cypari2/gen.pyx
>> > Hunk #1 succeeded at 141 (offset 6 lines).
>> > patching file cypari2/pari_instance.pyx
>> > ****************************************************
>> > Host system:
>> > Linux ural 4.9.0-9-amd64 #1 SMP Debian 4.9.168-1+deb9u4 (2019-07-19) 
>> > 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)
>> > ****************************************************
>> > Package 'cypari' is currently not installed
>> > No legacy uninstaller found for 'cypari'; nothing to do
>> > Installing cypari-2.1.1
>> > Installing package cypari2 using pip2
>> > Ignoring indexes: https://pypi.org/simple
>> > Created temporary directory: /tmp/pip-ephem-wheel-cache-4L98l9
>> > Created temporary directory: /tmp/pip-req-tracker-mosN7y
>> > Created requirements tracker '/tmp/pip-req-tracker-mosN7y'
>> > Created temporary directory: /tmp/pip-install-AHSkDU
>> > Processing 
>> > /srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src
>> >   Created temporary directory: /tmp/pip-req-build-eMwGZT
>> >   Added 
>> > file:///srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src 
>> > to build tracker '/tmp/pip-req-tracker-mosN7y'
>> >   Running setup.py (path:/tmp/pip-req-build-eMwGZT/setup.py) egg_info for 
>> > package from 
>> > file:///srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src
>> >     Running command python setup.py egg_info
>> >     running egg_info
>> >     creating pip-egg-info/cypari2.egg-info
>> >     writing requirements to pip-egg-info/cypari2.egg-info/requires.txt
>> >     writing pip-egg-info/cypari2.egg-info/PKG-INFO
>> >     writing top-level names to pip-egg-info/cypari2.egg-info/top_level.txt
>> >     writing dependency_links to 
>> > pip-egg-info/cypari2.egg-info/dependency_links.txt
>> >     writing manifest file 'pip-egg-info/cypari2.egg-info/SOURCES.txt'
>> >     error: [Errno 2] No such file or directory: '/usr/share/pari/pari.desc'
>> > Cleaning up...
>> >   Removing source in /tmp/pip-req-build-eMwGZT
>> > Removed 
>> > file:///srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1/src 
>> > from build tracker '/tmp/pip-req-tracker-mosN7y'
>> > Removed build tracker '/tmp/pip-req-tracker-mosN7y'
>> > Command "python setup.py egg_info" failed with error code 1 in 
>> > /tmp/pip-req-build-eMwGZT/
>> > Exception information:
>> > Traceback (most recent call last):
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py",
>> >  line 143, in main
>> >     status = self.run(options, args)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/commands/install.py",
>> >  line 318, in run
>> >     resolver.resolve(requirement_set)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
>> >  line 102, in resolve
>> >     self._resolve_one(requirement_set, req)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
>> >  line 256, in _resolve_one
>> >     abstract_dist = self._get_abstract_dist_for(req_to_install)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
>> >  line 209, in _get_abstract_dist_for
>> >     self.require_hashes
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
>> >  line 298, in prepare_linked_requirement
>> >     abstract_dist.prep_for_dist(finder, self.build_isolation)
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
>> >  line 126, in prep_for_dist
>> >     self.req.run_egg_info()
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py",
>> >  line 473, in run_egg_info
>> >     command_desc='python setup.py egg_info')
>> >   File 
>> > "/srv/public/shared/sage/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py",
>> >  line 705, in call_subprocess
>> >     % (command_desc, proc.returncode, cwd))
>> > InstallationError: Command "python setup.py egg_info" failed with error 
>> > code 1 in /tmp/pip-req-build-eMwGZT/
>> > Error: installing with pip2 failed
>> > ********************************************************************************
>> > Error installing cypari-2.1.1
>> > ********************************************************************************
>> >
>> > real    0m1.313s
>> > user    0m1.084s
>> > sys    0m0.176s
>> > ************************************************************************
>> > Error installing package cypari-2.1.1
>> > ************************************************************************
>> > Please email sage-devel (http://groups.google.com/group/sage-devel)
>> > explaining the problem and including the log file
>> >   /srv/public/shared/sage/logs/pkgs/cypari-2.1.1.log
>> > Describe your computer, operating system, etc.
>> > If you want to try to fix the problem yourself, *don't* just cd to
>> > /srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1 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 '/srv/public/shared/sage/local/var/tmp/sage/build/cypari-2.1.1' && 
>> > '/srv/public/shared/sage/sage' --sh)
>> > When you are done debugging, you can type "exit" to leave the subshell.
>> > ************************************************************************
>> >
>> >
>> > On Tuesday, September 3, 2019 at 1:22:40 AM UTC+2, Volker Braun wrote:
>> >>
>> >> As always, you can get the latest beta version from the "develop" git 
>> >> branch. Alternatively, the self-contained source tarball is at 
>> >> http://www.sagemath.org/download-latest.html
>> >>
>> >>
>> >> bdf4b23d74 (trac/develop, tag: 8.9.beta9) Updated SageMath version to 
>> >> 8.9.beta9
>> >> c631202c12 Trac #28411: refresh the prompt in the installation guide
>> >> 45482b13f0 Trac #28387: Implement function that returns the balanced 
>> >> digit representation of an integer
>> >> 4454ffec0d Trac #28384: py2: UnicodeDecodeError in doctest framework 
>> >> exception handling
>> >> 0c8192c3de Trac #28366: Lattice precision timing test fails on Windows 7 
>> >> due to low-ish clock resolution
>> >> 5e1b351a89 Trac #28274: EnumeratedFamily should use integers as keys
>> >> ec9715bb88 Trac #28172: Profile of a Finite Permutation Group
>> >> dcf58df8b5 Trac #28154: SciPy: patch for missing coding lines in some 
>> >> source files
>> >> 82d75fd335 Trac #27917: Standardize doctest headers
>> >> 04d5aab185 Trac #25817: RuntimeError: Encountered operator mismatch in 
>> >> maxima-to-sr translation, integrate
>> >> 45314bcbcf Trac #23639: Strange errors with roots() of polynomials over 
>> >> polynomial rings
>> >> f29cee985f Trac #28419: new pyflakes miscellanous cleanup
>> >> 77bddf472a Trac #28417: removed deprecated stuff in integer_mod
>> >> c565a3aa0a Trac #28412: upgrade Pynac to 0.7.26
>> >> 2e47b34ab8 Trac #28408: fixing a few invalid escape sequences
>> >> 877d26294b Trac #28407: py3: fix quantum_group_gap and graph_latex
>> >> 3db8be3dc0 Trac #28399: remove deprecated things in integer.pyx
>> >> 6a837c5ea6 Trac #27818: Meet-subsemilattice for lattices
>> >> 2920f66a0e Trac #27798: Add `backend` option to associahedron and flow 
>> >> polytope
>> >> 98f3199887 Trac #27587: Follow up to #25680: Fix tempfile handling in 
>> >> doctests
>> >> 0719be21c2 Trac #27473: Matrix inversion fails over a Laurent series ring
>> >> 842a3dcd41 Trac #27444: Expose multithreaded fflas-ffpack features
>> >> cee95e6b38 Trac #28404: Sign of hypergeometric motives is sometimes wrong
>> >> af8bf5ead8 Trac #28400: fixing a few roles
>> >> 1cdf4955c6 Trac #28398: _richcmp_ for quaternion algebra elements
>> >> abb2397287 Trac #28397: fix some wrong doctests that were not run
>> >> 2465a9e494 Trac #28396: faster Möbius matrix for Hasse diagrams
>> >> 4b4b5bf81b Trac #28395: Bug in is_weil_polynomial
>> >> 77466c5716 Trac #28393: add self-tests for polymake
>> >> a7f0a353e5 Trac #28391: dependencies file for jupymake
>> >> e7a3ec0d98 Trac #28377: polymake interface broken with "non-standard" 
>> >> quadratic fields
>> >> a535670711 Trac #28339: Random failure in src/sage/interfaces/expect.py
>> >> f34f77e4da Trac #28271: Implement LexM traversal
>> >> 304feb1626 Trac #28229: Generalized shifted prime tableau
>> >> e570374675 Trac #27689: Implement is_pyramid, is_bipyramid, is_prism for 
>> >> polytopes
>> >> addde7bcc7 Trac #28380: bump up the version of givaro in spkg-configure.m4
>> >> 8f1c30f031 Trac #28403: py3: crypto/block_cipher/present.py doctest 
>> >> failures
>> >> 0ae7ffa669 Trac #25727: Prevent giac from giving localized output
>> >> 109c1bd6c1 Trac #28060: Extensions of finite fields embeddings: we have 
>> >> inverse image but `inverse_image` throws `NotImplemented`
>> >> 0c5c45c0cf Trac #27937: Fix for functorial construction of monoid algebras
>> >> fee35bf412 Trac #27851: Convert sqrt(D) to UCF
>> >> 3b7ef2c62c Trac #27831: Small fix for is_symmetric for matrices over CDF
>> >> 8f76f4d242 Trac #27760: Generalized Permutohedra and type H4 4-uniform 
>> >> polytopes
>> >> 67de66d92d Trac #27096: Bug in Buchberger algorithm over Tate algebra
>> >> 6b8839d39f Trac #25823: maxima segfaults on integral computation
>> >> 4583b4056e (tag: 8.9.beta8, trac/develop) Updated SageMath version to 
>> >> 8.9.beta8
>> >>
>> > --
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>
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