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conda-forge / sage-feedstock

A conda-smithy repository for sage.
BSD 3-Clause "New" or "Revised" License
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Installing Normaliz causes sagelib downgrade 9.1 -> 9.0 #58

Closed NathanDunfield closed 4 years ago

NathanDunfield commented 4 years ago

Issue: Trying to install normaliz cause sagelib to be downgraded to from 9.1 to 9.0. Possibly sagelib 9.1 requires a newer version of normaliz?

$ mamba install normaliz
[...logo snipped...]
conda-forge/linux-64     Using cache
conda-forge/noarch       Using cache
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change

Looking for: ['normaliz']

Transaction

  Prefix: /data/keeling/a/nmd/miniconda3/envs/sage_full

  Updating specs:

   - normaliz

  Package    Version  Build             Channel                    Size
─────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────

  e-antic      0.1.7  h6f25847_0        conda-forge/linux-64     128 KB
  normaliz     3.8.1  hfa3ade1_3        conda-forge/linux-64       4 MB

  Change:
─────────────────────────────────────────────────────────────────────────

  arb         2.17.0  hbd1b91e_1        installed                      
  arb         2.17.0  h04dde30_0        conda-forge/linux-64     Cached
  eclib     20190909  hd99a102_2        installed                      
  eclib     20190909  h961da46_0        conda-forge/linux-64     Cached
  giac      1.5.0.63  hf51155a_6        installed                      
  giac      1.5.0.63  h07123c9_4        conda-forge/linux-64     Cached
  linbox       1.6.3  h4cae756_4        installed                      
  linbox       1.6.3  h03cd913_2        conda-forge/linux-64       3 MB
  pynac       0.7.26  py37h350d95b_5    installed                      
  pynac       0.7.26  py37h4fdf5a9_2    conda-forge/linux-64      27 MB
  singular  4.1.1.p2  ha188dad_4        installed                      
  singular  4.1.1.p2  h7f49944_2        conda-forge/linux-64      21 MB

  Downgrade:
─────────────────────────────────────────────────────────────────────────

  curl        7.71.1  he644dc0_3        installed                      
  curl        7.68.0  hf8cf82a_0        conda-forge/linux-64     Cached
  cvxopt       1.2.5  py37hf6e81e8_1    installed                      
  cvxopt       1.2.4  py37hcf54b7c_201  conda-forge/linux-64     Cached
  gsl            2.6  h294904e_0        installed                      
  gsl            2.5  h294904e_1        conda-forge/linux-64     Cached
  krb5        1.17.1  h173b8e3_0        installed                      
  krb5        1.16.4  h173b8e3_0        pkgs/main/linux-64       Cached
  libcurl     7.71.1  hcdd3856_3        installed                      
  libcurl     7.68.0  hda55be3_0        conda-forge/linux-64     Cached
  libflint     2.6.0  h6b702e8_0        installed                      
  libflint     2.5.2  h3fb3072_1003     conda-forge/linux-64     Cached
  ntl         11.4.3  h7b9faae_0        installed                      
  ntl         11.3.2  h4703815_1000     conda-forge/linux-64     Cached
  r-base       3.6.3  h316533a_2        installed                      
  r-base       3.6.2  h3a67422_0        conda-forge/linux-64      23 MB
  sage           9.1  py37hc8dfbb8_1    installed                      
  sage           9.0  py37_0            conda-forge/linux-64       6 KB
  sagelib        9.1  py37hbfcc262_0    installed                      
  sagelib        9.0  py37h360dde1_2    conda-forge/linux-64      87 MB
  three.js       110  0                 installed                      
  three.js       105  0                 conda-forge/noarch         4 MB
  tornado      6.0.4  py37h7b6447c_1    installed                      
  tornado      4.5.3  py37_0            pkgs/main/linux-64       575 KB

  Summary:

  Install: 2 packages
  Change: 6 packages
  Downgrade: 12 packages

  Total download: 169 MB

─────────────────────────────────────────────────────────────────────────


Environment (conda list): Clean install mamba install --name=sage_full sage python=3.7.

``` $ conda list # packages in environment at /data/keeling/a/nmd/miniconda3/envs/sage_full: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 0_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge alabaster 0.7.12 py37_0 alsa-lib 1.2.3 h516909a_0 conda-forge appdirs 1.4.3 py37h28b3542_0 arb 2.17.0 hbd1b91e_1 conda-forge attrs 19.3.0 py_0 automat 20.2.0 py_0 conda-forge babel 2.8.0 py_0 bdw-gc 8.0.4 hc9558a2_0 conda-forge binutils_impl_linux-64 2.34 h53a641e_7 conda-forge binutils_linux-64 2.34 hc952b39_20 conda-forge blas 1.1 openblas conda-forge bleach 3.1.5 py_0 brial 1.2.7 py_1 conda-forge brotlipy 0.7.0 py37h7b6447c_1000 bwidget 1.9.14 0 conda-forge bzip2 1.0.8 h7b6447c_0 ca-certificates 2020.6.24 0 cairo 1.16.0 hcf35c78_1003 conda-forge cddlib 1!0.94j he80fd80_1001 conda-forge certifi 2020.6.20 py37_0 cffi 1.14.0 py37h2e261b9_0 chardet 3.0.4 py37_1003 click 7.1.2 py_0 cliquer 1.21 h516909a_1001 conda-forge constantly 15.1.0 py37h28b3542_0 cryptography 3.0 py37hb09aad4_0 conda-forge curl 7.71.1 he644dc0_3 conda-forge cvxopt 1.2.5 py37hf6e81e8_1 conda-forge cycler 0.10.0 py37_0 cypari2 2.1.1 py37hef3d0d6_1 conda-forge cysignals 1.10.2 py37he8bbba0_1 conda-forge cython 0.29.21 py37he6710b0_0 decorator 4.4.2 py_0 defusedxml 0.6.0 py_0 docutils 0.16 py37_1 dsdp 5.8 h75fe3a5_0 ecl 16.1.2 h33275a5_1004 conda-forge eclib 20190909 hd99a102_2 conda-forge ecm 7.0.4 he80fd80_1002 conda-forge entrypoints 0.3 py37_0 expat 2.2.9 he6710b0_2 fastcache 1.1.0 py37h7b6447c_0 fflas-ffpack 2.4.3 h5896f46_1 conda-forge fftw 3.3.8 h7b6447c_3 flask 0.11.1 py_1 conda-forge flask-autoindex 0.6.2 py_0 conda-forge flask-babel 0.12.2 py_1 flask-oldsessions 0.10 py_0 conda-forge flask-openid 1.2.5 py37_1003 flask-silk 0.2 py_0 conda-forge flintqs 1.0 h79a8f9a_1000 conda-forge fontconfig 2.13.1 h86ecdb6_1001 conda-forge fplll 5.3.1 hb70a6f5_0 conda-forge fpylll 0.5.1dev py37h03658f4_0 conda-forge freetype 2.10.2 h5ab3b9f_0 fribidi 1.0.10 h516909a_0 conda-forge future 0.18.2 py37_1 fxrays 1.3.3 pypi_0 pypi gap-core 4.10.2 h8c737de_5 conda-forge gap-defaults 4.10.2 5 conda-forge gcc_impl_linux-64 7.5.0 hd420e75_6 conda-forge gcc_linux-64 7.5.0 h09487f9_20 conda-forge gettext 0.19.8.1 hd7bead4_3 gf2x 1.2 ha03fbb7_1003 conda-forge gfan 0.6.2 h192cbe9_1002 conda-forge gfortran_impl_linux-64 7.5.0 hdf63c60_6 conda-forge gfortran_linux-64 7.5.0 h09487f9_20 conda-forge giac 1.5.0.63 hf51155a_6 conda-forge giflib 5.2.1 h516909a_2 conda-forge givaro 4.1.1 h192cbe9_0 conda-forge glib 2.65.0 h6f030ca_0 conda-forge glpk 4.65 h3ceedfd_2 gmp 6.2.0 he1b5a44_2 conda-forge gmpy2 2.1.0b1 py37h04dde30_0 conda-forge graphite2 1.3.14 h23475e2_0 gsl 2.6 h294904e_0 conda-forge gxx_impl_linux-64 7.5.0 hdf63c60_6 conda-forge gxx_linux-64 7.5.0 h09487f9_20 conda-forge harfbuzz 2.4.0 h9f30f68_3 conda-forge hyperlink 19.0.0 py_0 icu 64.2 he1b5a44_1 conda-forge idna 2.10 py_0 imagesize 1.2.0 py_0 iml 1.0.5 h3057dec_1002 conda-forge importlib-metadata 1.7.0 py37_0 importlib_metadata 1.7.0 0 incremental 17.5.0 py37_0 ipykernel 4.10.0 py37_0 ipython 5.8.0 py37_0 ipython_genutils 0.2.0 py37_0 ipywidgets 7.5.1 py_0 itsdangerous 1.1.0 py37_0 jinja2 2.10.3 py_0 jmol 14.29.15 2 conda-forge jpeg 9d h516909a_0 conda-forge jsonschema 3.0.0a3 py37_1000 conda-forge jupyter_client 5.3.4 py37_0 jupyter_core 4.6.3 py37_0 kiwisolver 1.2.0 py37hfd86e86_0 krb5 1.17.1 h173b8e3_0 lcalc 1.23 hab5a3d0_1004 conda-forge lcms2 2.11 h396b838_0 ld_impl_linux-64 2.34 h53a641e_7 conda-forge libblas 3.8.0 17_openblas conda-forge libbraiding 1.0 he1b5a44_0 conda-forge libbrial 1.2.7 hf4f5a66_1 conda-forge libcblas 3.8.0 17_openblas conda-forge libcurl 7.71.1 hcdd3856_3 conda-forge libedit 3.1.20191231 h14c3975_1 libffi 3.2.1 hd88cf55_4 libflint 2.6.0 h6b702e8_0 conda-forge libgcc-ng 9.2.0 h24d8f2e_2 conda-forge libgd 2.2.5 h307a58e_1007 conda-forge libgfortran-ng 7.5.0 hdf63c60_6 conda-forge libgomp 9.2.0 h24d8f2e_2 conda-forge libhomfly 1.02r6 h516909a_0 conda-forge libiconv 1.15 h63c8f33_5 liblapack 3.8.0 17_openblas conda-forge liblapacke 3.8.0 17_openblas conda-forge libopenblas 0.3.10 h5a2b251_0 libpng 1.6.37 hbc83047_0 libsodium 1.0.18 h7b6447c_0 libssh2 1.9.0 h1ba5d50_1 libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge libtiff 4.1.0 h2733197_1 libuuid 2.32.1 h14c3975_1000 conda-forge libwebp 1.0.2 h56121f0_5 conda-forge libxcb 1.14 h7b6447c_0 libxml2 2.9.10 hee79883_0 conda-forge linbox 1.6.3 h4cae756_4 conda-forge lrcalc 1.2 hf484d3e_1000 conda-forge lz4-c 1.9.2 he6710b0_0 m4ri 20140914 he06d7ca_1005 conda-forge m4rie 20150908 he06d7ca_1001 conda-forge make 4.3 h516909a_0 conda-forge markupsafe 1.1.1 py37h14c3975_1 matplotlib-base 2.2.5 py37h250f245_1 conda-forge maxima 5.42.2 h33275a5_2 conda-forge metis 5.1.0 hf484d3e_4 mistune 0.8.4 py37h14c3975_1001 mpc 1.1.0 h10f8cd9_1 mpfi 1.5.4 hb20f59a_1001 conda-forge mpfr 4.0.2 hb69a4c5_1 mpmath 1.1.0 py37_0 nauty 2.6.11 h516909a_1 conda-forge nbconvert 5.6.1 py37_1 nbformat 4.4.0 py37_0 ncurses 6.2 he6710b0_1 networkx 2.4 py_1 notebook 5.7.10 py37hc8dfbb8_0 conda-forge ntl 11.4.3 h7b9faae_0 conda-forge numpy 1.19.1 py37h8960a57_0 conda-forge olefile 0.46 py37_0 openblas 0.3.4 h9ac9557_1000 conda-forge openjdk 11.0.1 hacce0ff_1021 conda-forge openssl 1.1.1g h7b6447c_0 packaging 20.4 py_0 palp 2.1 h516909a_1001 conda-forge pandoc 2.10.1 h516909a_0 conda-forge pandocfilters 1.4.2 py37_1 pango 1.42.4 h7062337_4 conda-forge pari 2.11.2 pl526h80ae19e_0 conda-forge pari-galdata 0.0.20180411 0 conda-forge pari-seadata-small 0.0.20090618 0 conda-forge path 13.1.0 py37_0 path.py 12.4.0 0 pathlib2 2.3.5 py37_1 pcre 8.44 he6710b0_0 perl 5.26.2 h14c3975_0 pexpect 4.8.0 py37_1 pickleshare 0.7.5 py37_1001 pillow 5.4.1 py37h34e0f95_0 pip 20.1.1 py37_1 pixman 0.38.0 h7b6447c_0 pkg-config 0.29.2 h1bed415_8 pkgconfig 1.4.0 py37_0 planarity 3.0.0.5 h516909a_1002 conda-forge plink 2.3.1 pypi_0 pypi ppl 1.2 h618b193_1003 conda-forge pplpy 0.8.4 py37h9603a25_0 conda-forge prometheus_client 0.8.0 py_0 prompt_toolkit 1.0.15 py37_0 psutil 5.7.2 py37h8f50634_0 conda-forge ptyprocess 0.6.0 py37_0 pyasn1 0.4.8 py_0 pyasn1-modules 0.2.7 py_0 pycparser 2.20 py_2 pygments 2.6.1 py_0 pyhamcrest 2.0.2 py_0 pynac 0.7.26 py37h350d95b_5 conda-forge pyopenssl 19.1.0 py37_0 pyparsing 2.4.7 py_0 pypng 0.0.20 pypi_0 pypi pyrsistent 0.16.0 py37h7b6447c_0 pysocks 1.7.1 py37_1 python 3.7.8 h425cb1d_0_cpython conda-forge python-dateutil 2.8.1 py_0 python3-openid 3.1.0 py37_1001 python_abi 3.7 1_cp37m conda-forge pytz 2020.1 py_0 pyzmq 18.1.1 py37he6710b0_0 qd 2.3.22 hc99cbb1_1003 conda-forge r-base 3.6.3 h316533a_2 conda-forge ratpoints 2.1.3 he80fd80_1002 conda-forge readline 8.0 h7b6447c_0 requests 2.24.0 py_0 rpy2 3.3.2 py37r36h03ebfcd_0 conda-forge rubiks 20070912 hf484d3e_1001 conda-forge rw 0.7 1 conda-forge sage 9.1 py37hc8dfbb8_1 conda-forge sagelib 9.1 py37hbfcc262_0 conda-forge sagemath-db-combinatorial-designs 20140630 0 conda-forge sagemath-db-conway-polynomials 0.5.0 py37hecc5488_0 conda-forge sagemath-db-elliptic-curves 0.8.1 hecc5488_0 conda-forge sagemath-db-graphs 20161026 0 conda-forge sagemath-db-polytopes 20170220 0 conda-forge sagenb 1.1.3 py_0 conda-forge sagetex 3.4 py_0 conda-forge scipy 1.5.2 py37hb14ef9d_0 conda-forge sed 4.8 hbfbb72e_0 conda-forge send2trash 1.5.0 py37_0 service_identity 18.1.0 py37h28b3542_0 setuptools 49.2.0 py37_0 simplegeneric 0.8.1 py37_2 singledispatch 3.4.0.3 py37_0 singular 4.1.1.p2 ha188dad_4 conda-forge six 1.15.0 py_0 snappy 2.8 pypi_0 pypi snappy-manifolds 1.1.1 pypi_0 pypi snowballstemmer 2.0.0 py_0 spherogram 1.8.3 pypi_0 pypi sphinx 1.8.5 py37_0 sphinxcontrib 1.0 py37_1 sphinxcontrib-websupport 1.2.3 py_0 sqlite 3.32.3 h62c20be_0 suitesparse 5.7.2 h717dc36_0 conda-forge symmetrica 2.0 he1b5a44_1007 conda-forge sympow 2.023.3 h4c5a542_1003 conda-forge sympy 1.5.1 py37_0 tachyon 0.99b6 hdfe0703_1001 conda-forge tbb 2020.1 hc9558a2_0 conda-forge terminado 0.8.3 py37_0 testpath 0.4.4 py_0 three.js 110 0 conda-forge tk 8.6.10 hbc83047_0 tktable 2.10 h14c3975_0 tornado 6.0.4 py37h7b6447c_1 traitlets 4.3.3 py37_0 twisted 18.9.0 py37h7b6447c_0 tzlocal 2.1 pyh9f0ad1d_0 conda-forge urllib3 1.25.10 py_0 conda-forge wcwidth 0.2.5 py_0 webencodings 0.5.1 py37_1 werkzeug 1.0.1 py_0 wheel 0.34.2 py37_0 widgetsnbextension 3.5.1 py37_0 xorg-fixesproto 5.0 h14c3975_1002 conda-forge xorg-inputproto 2.3.2 h14c3975_1002 conda-forge xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.9 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxfixes 5.0.3 h516909a_1004 conda-forge xorg-libxi 1.7.10 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-libxtst 1.2.3 h516909a_1002 conda-forge xorg-recordproto 1.14.2 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.5 h7b6447c_0 zeromq 4.3.2 he6710b0_2 zipp 3.1.0 py_0 zlib 1.2.11 h7b6447c_3 zn_poly 0.9.2 he80fd80_0 conda-forge zope.interface 5.1.0 py37h8f50634_0 conda-forge zstd 1.4.5 h0b5b093_0 ```


Details about conda and system ( conda info ):

``` $ conda info active environment : sage_full active env location : /data/keeling/a/nmd/miniconda3/envs/sage_full shell level : 2 user config file : /data/keeling/a/nmd/.condarc populated config files : /data/keeling/a/nmd/.condarc conda version : 4.8.3 conda-build version : not installed python version : 3.7.7.final.0 virtual packages : __glibc=2.12 base environment : /data/keeling/a/nmd/miniconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch package cache : /data/keeling/a/nmd/miniconda3/pkgs /data/keeling/a/nmd/.conda/pkgs envs directories : /data/keeling/a/nmd/miniconda3/envs /data/keeling/a/nmd/.conda/envs platform : linux-64 user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.7 Linux/2.6.32-754.30.2.el6.x86_64 scientific/6.10 glibc/2.12 UID:GID : 436808:1549047 netrc file : None offline mode : False ```
isuruf commented 4 years ago

Thanks for the report. There was a failing build and restarting it fixed the issue.

NathanDunfield commented 4 years ago

Many thanks, I was able to install normaliz with Sage 9.1. To get PyNormaliz so that e.g.:

sage: P = Polyhedron(vertices=[[0,1], [1,0]], backend='normaliz', base_ring=QQ)

works, I had to do sage -pip install pynormaliz as the usual sage -i pynormaliz gave the error:

make: *** No rule to make target 'all-toolchain'.  Stop.
isuruf commented 4 years ago

You are welcome. Yes, sage -i doesn't work and would be disabled in a future release, so that the error message is not confusing.