conda-forge / sage-feedstock

A conda-smithy repository for sage.

About sage-feedstock

Feedstock license: BSD-3-Clause

Home: http://sagemath.org

Package license: GPL-2.0-or-later

Summary: Sage - Open Source Mathematical Software

Development: https://github.com/sagemath/sage

Documentation: https://doc.sagemath.org/

Creating a Viable Open Source Alternative to Magma, Maple, Mathematica, and MATLAB.

Current build status

All platforms:

Current release info

Name	Downloads	Version	Platforms

Installing sage

Installing sage from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, sage can be installed with conda:

conda install sage

or with mamba:

mamba install sage

It is possible to list all of the versions of sage available on your platform with conda:

conda search sage --channel conda-forge

or with mamba:

mamba search sage --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search sage --channel conda-forge

# List packages depending on `sage`:
mamba repoquery whoneeds sage --channel conda-forge

# List dependencies of `sage`:
mamba repoquery depends sage --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating sage-feedstock

If you would like to improve the sage recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/sage-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @alexjbest
• @isuruf
• @saraedum

sage-feedstock's Issues

Move version pinnings from this recipe to sagelib

See conda-forge/sagelib-feedstock#46. Pinnings should go as low in the dependency tree as possible. Right now, if you install just sagelib (to save some space compared to the full sage), some packages will be broken because it doesn't have the right version pinnings.

sagemath 8.x does not install on fresh miniconda

Issue: Sagemath does not install on a fresh 'miniconda' distribution because of a package versioning issue

To reproduce:
Install fresh miniconda distribution (python 2.7)
Perform step 1 and 2 of https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda (add conda-forge source, update)
Attempt to install the most recent sage by version (conda create -v -n sage sage=8.3[build=py27_3])

Failure:

PackagesNotFoundError: The following packages are not available from current channels:

• sage=8.3[build=py27_3] -> sagemath-db-conway-polynomials[version='>=0.5.*']

Specifically, the version number 0.5.p0 for sagemath-db-conway-polynomials does not appear to match the >=0.5.* specifier.

Conda version: conda 4.6.8

Installation on Macbook Pro M2 fails

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

I installed SageMath through conda-forge on my new M2 Macbook Pro following the instructions, but the installation is incomplete. Specifically, I am getting a warning that sage.all is not available and that this is a limited REPL. When I try to import sage.all I am getting a weird error like this:

ImportError: dlopen(/opt/homebrew/anaconda3/envs/sage/lib/python3.10/site-packages/sage/libs/linbox/linbox_flint_interface.cpython-310-darwin.so, 0x0002): symbol not found in flat namespace '__ZN6FFPACK8CharPolyIN6Givaro8Poly1DomINS1_7ModularIddvEENS1_5DenseEEEEERNT_7ElementERKS7_S9_mNS7_8Domain_t11Element_ptrEmRNSC_8RandIterENS_19FFPACK_CHARPOLY_TAGEm'

The same happens when I try to open a jupyter notebook with sage's kernel.

Installed packages

packages in environment at /Users/giorgos/miniforge3/envs/sage:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
anyio                     3.7.0              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
arb                       2.23.0               he5401aa_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py311he2be06e_3    conda-forge
arpack                    3.7.0                h58ebc17_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bdw-gc                    8.0.6                hc021e02_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
beniget                   0.4.1              pyhd8ed1ab_0    conda-forge
blas-devel                3.9.0           16_osxarm64_openblas    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
brial                     1.2.12             pyha3edaa6_0    conda-forge
brotli                    1.0.9                h1a8c8d9_8    conda-forge
brotli-bin                1.0.9                h1a8c8d9_8    conda-forge
bwidget                   1.9.14               hce30654_1    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.19.1               hb547adb_0    conda-forge
ca-certificates           2023.5.7             hf0a4a13_0    conda-forge
cairo                     1.16.0            h73a0509_1014    conda-forge
cctools_osx-arm64         973.0.1             hcdc440c_13    conda-forge
cddlib                    1!0.94m              h6d7a090_0    conda-forge
certifi                   2023.5.7           pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py311hae827db_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
clang                     15.0.7               hce30654_2    conda-forge
clang-15                  15.0.7          default_h5dc8d65_2    conda-forge
clang_osx-arm64           15.0.7               h77e971b_3    conda-forge
clangxx                   15.0.7          default_h610c423_2    conda-forge
clangxx_osx-arm64         15.0.7               h768a7fd_3    conda-forge
cliquer                   1.22                 h27ca646_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
compiler-rt               15.0.7               hf8d1dfb_1    conda-forge
compiler-rt_osx-arm64     15.0.7               hf8d1dfb_1    conda-forge
contourpy                 1.0.7           py311hd6ee22a_0    conda-forge
curl                      8.1.2                h912dcd9_0    conda-forge
cvxopt                    1.3.1           py311hd76776f_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cypari2                   2.1.3           py311h149620a_2    conda-forge
cysignals                 1.11.2          py311he42fc87_2    conda-forge
cython                    0.29.35         py311ha891d26_0    conda-forge
debugpy                   1.6.7           py311ha397e9f_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.19            py311h267d04e_1    conda-forge
dsdp                      5.8               h9397a75_1203    conda-forge
ecl                       21.2.1               h8492d4d_2    conda-forge
eclib                     20230424             haeb5157_0    conda-forge
ecm                       7.0.4             h47c7c1a_1002    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hb7217d7_1    conda-forge
fflas-ffpack              2.4.3                h11f2abc_2    conda-forge
fftw                      3.3.10          nompi_h3046061_107    conda-forge
flintqs                   1.0               ha2e105b_1001    conda-forge
flit-core                 3.9.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.4          py311heffc1b2_0    conda-forge
fplll                     5.4.4                h29209e0_0    conda-forge
fpylll                    0.5.9           py311h3ca9eb5_1    conda-forge
freetype                  2.12.1               hd633e50_1    conda-forge
fribidi                   1.0.10               h27ca646_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gap-core                  4.12.2               he8f4e70_3    conda-forge
gap-defaults              4.12.2               hce30654_3    conda-forge
gast                      0.5.3              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h0186832_0    conda-forge
gf2x                      1.3.0                hdaa854c_2    conda-forge
gfan                      0.6.2             hec08f5c_1003    conda-forge
gfortran_impl_osx-arm64   12.2.0              hf7539cf_31    conda-forge
gfortran_osx-arm64        12.2.0               h57527a5_1    conda-forge
giac                      1.9.0.21             h1c96721_1    conda-forge
giflib                    5.2.1                h1a8c8d9_3    conda-forge
givaro                    4.1.1                h76d1151_2    conda-forge
glpk                      5.0                  h6d7a090_0    conda-forge
gmp                       6.2.1                h9f76cd9_0    conda-forge
gmpy2                     2.1.2           py311h2ba9262_1    conda-forge
graphite2                 1.3.13            h9f76cd9_1001    conda-forge
gsl                       2.7                  h6e638da_0    conda-forge
harfbuzz                  6.0.0                hddbc195_0    conda-forge
icu                       70.1                 h6b3803e_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
igraph                    0.9.10               hcec9b84_1    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
iml                       1.0.5             hd52f0d1_1003    conda-forge
importlib-metadata        6.6.0              pyha770c72_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.23.1             pyh736e0ef_0    conda-forge
ipython                   8.13.2             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.6              pyhd8ed1ab_0    conda-forge
isl                       0.25                 h9a09cb3_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jmol                      14.32.10             hce30654_0    conda-forge
jpeg                      9e                   h1a8c8d9_3    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_core              4.12.0          py311h267d04e_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.6.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.7              pyhd8ed1ab_1    conda-forge
kiwisolver                1.4.4           py311hd6ee22a_1    conda-forge
krb5                      1.20.1               h69eda48_0    conda-forge
lcalc                     2.0.5                hc94e8e6_1    conda-forge
lcms2                     2.15                 h481adae_0    conda-forge
ld64_osx-arm64            609                 h74cdc5f_13    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libbraiding               1.1                  h9f76cd9_0    conda-forge
libbrial                  1.2.12               he94e455_0    conda-forge
libbrotlicommon           1.0.9                h1a8c8d9_8    conda-forge
libbrotlidec              1.0.9                h1a8c8d9_8    conda-forge
libbrotlienc              1.0.9                h1a8c8d9_8    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libclang-cpp15            15.0.7          default_h5dc8d65_2    conda-forge
libcurl                   8.1.2                h912dcd9_0    conda-forge
libcxx                    16.0.4               h4653b0c_0    conda-forge
libdeflate                1.17                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libexpat                  2.5.0                hb7217d7_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libflint                  2.9.0           h173eafc_ntl_100    conda-forge
libgd                     2.3.3                h90fb8ed_4    conda-forge
libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
libgfortran-devel_osx-arm64 12.2.0              he825656_31    conda-forge
libgfortran5              12.2.0              h0eea778_31    conda-forge
libglib                   2.76.3               h24e9cb9_0    conda-forge
libhomfly                 1.02r6               h27ca646_0    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
liblapacke                3.9.0           16_osxarm64_openblas    conda-forge
libllvm15                 15.0.7               h62b9111_1    conda-forge
libnghttp2                1.52.0               hae82a92_0    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.42.0               hb31c410_0    conda-forge
libssh2                   1.10.0               h7a5bd25_3    conda-forge
libtiff                   4.5.0                h5dffbdd_2    conda-forge
libwebp                   1.2.4                h999c80f_1    conda-forge
libwebp-base              1.2.4                h1a8c8d9_0    conda-forge
libxcb                    1.13              h9b22ae9_1004    conda-forge
libxml2                   2.10.3               h67585b2_4    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
linbox                    1.6.3                h549c411_7    conda-forge
llvm-openmp               16.0.4               h1c12783_0    conda-forge
llvm-tools                15.0.7               h62b9111_1    conda-forge
lrcalc                    2.1                  hb7217d7_5    conda-forge
m4ri                      20140914          h17b34a0_1005    conda-forge
m4rie                     20150908          h17b34a0_1001    conda-forge
make                      4.3                  he57ea6c_1    conda-forge
markupsafe                2.1.2           py311he2be06e_0    conda-forge
matplotlib-base           3.7.1           py311h99a5f44_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
maxima                    5.45.0               h6032a66_2    conda-forge
memory-allocator          0.1.2           py311he2be06e_2    conda-forge
metis                     5.1.0             h9f76cd9_1006    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                h91ba8db_0    conda-forge
mpfi                      1.5.4             hbde5f5b_1001    conda-forge
mpfr                      4.2.0                he09a6ba_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nauty                     2.7.2                h3422bc3_0    conda-forge
nbclassic                 1.0.0              pyhb4ecaf3_1    conda-forge
nbclient                  0.7.4              pyhd8ed1ab_0    conda-forge
nbconvert                 7.4.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.4.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.4.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  2.8.8              pyhd8ed1ab_0    conda-forge
notebook                  6.5.4              pyha770c72_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
ntl                       11.4.3               hbb3f309_1    conda-forge
numpy                     1.24.3          py311hb8f3215_0    conda-forge
openblas                  0.3.21          openmp_hf78f355_3    conda-forge
openjdk                   17.0.3               hbe7ddab_8    conda-forge
openjpeg                  2.5.0                hbc2ba62_2    conda-forge
openssl                   3.1.0                h53f4e23_3    conda-forge
overrides                 7.3.1              pyhd8ed1ab_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
palp                      2.20                 h27ca646_0    conda-forge
pandoc                    2.19.2               hce30654_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.14              h6c112b8_0    conda-forge
pari                      2.15.3          hee76a8e_2_pthread    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hb34f9b4_0    conda-forge
perl                      5.32.1          2_h9b22ae9_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0           py311h627eb56_1    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h27ca646_0    conda-forge
pkg-config                0.29.2            hab62308_1008    conda-forge
pkgconfig                 1.5.5              pyhd8ed1ab_4    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
planarity                 3.0.0.5           h27ca646_1002    conda-forge
platformdirs              3.5.1              pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
ppl                       1.2               h8b147cf_1006    conda-forge
pplpy                     0.8.7           py311hb546c2d_0    conda-forge
primecount                7.6                  hb6e4faa_0    conda-forge
primecountpy              0.1.0           py311he4fd1f5_3    conda-forge
primesieve                11.0                 hb7217d7_0    conda-forge
prometheus_client         0.17.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.5           py311he2be06e_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.15.1             pyhd8ed1ab_0    conda-forge
pyobjc-core               9.1.1           py311h490943d_0    conda-forge
pyobjc-framework-cocoa    9.1.1           py311h490943d_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py311he2be06e_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.11.3          h1456518_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.17.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-lrcalc             2.1             py311ha397e9f_5    conda-forge
python_abi                3.11                    3_cp311    conda-forge
pythran                   0.12.2          py311hddbb800_1    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0             py311he2be06e_5    conda-forge
pyzmq                     24.0.1          py311h0f351f6_1    conda-forge
qd                        2.3.22            hbec66e7_1004    conda-forge
r-base                    4.1.3                h9c4d319_6    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpy2                      3.5.11          py311r41h4add359_0    conda-forge
rubiks                    20070912          h9f76cd9_1001    conda-forge
rw                        0.9                  h3422bc3_0    conda-forge
sage                      10.0                 hd8ed1ab_0    conda-forge
sage-docbuild             10.0                     pypi_0    pypi
sage-setup                10.0                     pypi_0    pypi
sagelib                   10.0            py311ha07c8a7_0    conda-forge
sagemath-db-combinatorial-designs 20140630                      1    conda-forge
sagemath-db-conway-polynomials 0.5.0                h4653dfc_1    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20210214             hd8ed1ab_0    conda-forge
sagemath-db-polytopes     20170220                      1    conda-forge
sagemath-standard         10.0                     pypi_0    pypi
sagetex                   3.6.1              pyhd8ed1ab_0    conda-forge
scipy                     1.10.1          py311h93d07a4_3    conda-forge
send2trash                1.8.2              pyhd1c38e8_0    conda-forge
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
sigtool                   0.1.3                h44b9a77_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singular                  4.2.1.p3             hb77faed_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sphinx                    5.3.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlite                    3.42.0               h203b68d_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
suitesparse               5.10.1               h7cd81ec_1    conda-forge
symmetrica                3.0.1                hb7217d7_0    conda-forge
sympow                    2.023.6              hb0babe8_3    conda-forge
sympy                     1.12            pypyh9d50eac_103    conda-forge
tachyon                   0.99b6            hfb72b2a_1001    conda-forge
tapi                      1100.0.11            he4954df_0    conda-forge
tbb                       2021.9.0             hffc8910_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
three.js                  122                  hd8ed1ab_2    conda-forge
threejs-sage              122                  hd8ed1ab_2    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tktable                   2.10                 h4161312_3    conda-forge
tornado                   6.3.2           py311heffc1b2_0    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.6.2                hd8ed1ab_0    conda-forge
typing_extensions         4.6.2              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
tzlocal                   5.0.1           py311h267d04e_0    conda-forge
urllib3                   2.0.2              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.2              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.7              pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hb547adb_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zeromq                    4.3.4                hbdafb3b_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h03a7124_4    conda-forge
zn_poly                   0.9.2                h391046e_0    conda-forge
zstd                      1.5.2                hf913c23_6    conda-forge

Environment info

active environment : sage
    active env location : /Users/giorgos/miniforge3/envs/sage
            shell level : 2
       user config file : /Users/giorgos/.condarc
 populated config files : /Users/giorgos/miniforge3/.condarc
                          /Users/giorgos/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=arm64
                          __osx=13.2.1=0
                          __unix=0=0
       base environment : /Users/giorgos/miniforge3  (writable)
      conda av data dir : /Users/giorgos/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/giorgos/miniforge3/pkgs
                          /Users/giorgos/.conda/pkgs
       envs directories : /Users/giorgos/miniforge3/envs
                          /Users/giorgos/.conda/envs
               platform : osx-arm64
             user-agent : conda/23.1.0 requests/2.28.2 CPython/3.10.10 Darwin/22.3.0 OSX/13.2.1
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Not functional installation of sage 9.7

Comment:

I installed sage 9.7 via conda-forge and my installation of sage does not work, as explained in this post.

My OS is Ubuntu 18.04. First, I installed mamba using the instructions found here.

Then, following the instruction here, I created the sage environment with this command line:

mamba create -n sage sage python=3.9

Then I activated it like this

(base) po@po-ta:~$ conda activate sage

Finally I ran sage:

(sage) po@po-ta:~$ sage

Here is the entire screen output I got:

(sage) po@po-ta:~$ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.7, Release Date: 2022-09-19                     │
│ Using Python 3.9.13. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: sage.all is not available; this is a limited REPL.        ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: 

The sage installation is not functional as the warning explains.

Cannot install sage with nodefaults

I am trying to create an environment.yml to build SageMath documentation on ReadTheDocs at MCLF/mclf#107.

I thought it would be a good idea to take only packages from conda-forge and non from default so I wrote:

name: readthedocs
channels:
  - conda-forge
  - nodefaults
dependencies:
  - sage=8.3

However, this makes sage=8.3 unsatisfiable. Dropping the nodefaults line, pulls in these default packages

cairo                     1.14.12              h7636065_2
harfbuzz                  1.7.6                h5f0a787_1
libgcc-ng                 8.2.0                hdf63c60_1
libopenblas               0.3.3                h5a2b251_3
numpy                     1.15.4           py36h99e49ec_0
numpy-base                1.15.4           py36h2f8d375_0
qt                        5.6.2               h974d657_12  

It's probably not a big deal but still I am wondering why dependencies cannot be satisfied from conda-forge here? In particular I am not sure about mixing libopenblas from default and our packages.

I noted that already during the sage build some packages from default were used during testing but that's probably normal https://circleci.com/gh/conda-forge/sage-feedstock/118:

    cairo:                             1.14.12-h77bcde2_0                   defaults   
    glib:                              2.53.6-h5d9569c_2                    defaults   
    gmpy2:                             2.0.8-py36h10f8cd9_2                 defaults
    gstreamer:                         1.12.4-hb53b477_0                    defaults
    harfbuzz:                          1.7.6-hc5b324e_0                     defaults
    openjdk:                           8.0.152-h46b5887_1                   defaults
    qt:                                5.6.2-hd25b39d_14                    defaults

pinnings

I see at least boost, sqlite not pinned here

Upgrade to 8.3

The list of packages has been compiled with git diff 8.2..8.3 build/.

🤔: These packages are probably not the right version in conda-forge but they should not matter for the conda release.

Base SPKGs that have changed.

none.

Standard SPKGs that have changed.

• arb (2.12.0.p0 → 2.13.0.p0), adds arb-acosh.patch, drops arb-pie-hardening-conflict.patch
• cddlib (094g.p2 → 094i), conda-forge/cddlib-feedstock#6
• 🤔 cmake (3.8.1 → 3.11.0)
• combinatorial_designs (20140630 → 20140630.p0), install script changes
• configure (262 → 272)
• curl (7.56.1 → 7.56.1.p0)
• cysignals (1.7.0.p0 → 1.7.2), drops stack_guard.patch
• fflas_ffpack (no version change), adds 25353-flasffpack-constvoid.patch
• fplll (5.2.0.p1 → 5.2.1), drops GCC.patch, pow.patch
• fpylll (0.3.0dev.p0 → 0.4.1dev), drops ticket-24191.patch, conda-forge/fpylll-feedstock#6
• freetype (2.8.1 → 2.8.1.p0), build script changes
• gc (7.6.4 → 7.6.4.p0), build script changes
• gfan (0.5.p2 →0.6.2.p0), lots of patch changes; conda-forge/gfan-feedstock#7
• graphs (20161026 → 20161026.p0), build script changes
• ipython (5.5.0 → 5.5.0.p0), adds signature.patch. (Needs to apply the patch to 5.x branch on feedstock)
• ipywidgets (7.1.1 → 7.2.0)
• mathjax (2.6.1 → 2.7.4), drops extend_maxbuffer.patch, nopng_config.patch
• maxima (5.39.0.p2 → 5.41.0)
• nauty (26r1 → 26r1.p0)
• NetworkX (1.11.p0 → 2.1)
• NTL (10.3.0 → 10.3.0.p0), build script changes
• OpenBLAS (0.2.20.p1 → 0.2.20.p2), Sparc changes
• pari (2.10-1280-g88fb5b3.p0 → 2.10-1280-g88fb5b3.p1), modified stackwarn.patch
• pari_galdata (20080411 → 20080411.p0), modifies build scripts
• pari_seadata_small (20090618 → 20090618.p0), modifies build scripts
• polytopes_db (20170220 → 20170220.p0), modified build scripts
• 🤔pycygwin
• pynac (0.7.16.p0 → 0.7.22), unpatched now, conda-forge/pynac-feedstock#12
• 🤔 python (2.7.14.p2 → 2.7.15)
• 🤔R (3.4.3.p0 → 3.4.4.p0),
• sagenb (1.0.1 → 1.0.3)
• sphinx (1.6.3.p1 → 1.7.5.p0), adds GH-5040.patch, drops unpickle_error.patch
• tachyon, build script changes
• thebe (9624e0a0 → 9624e0a0.p0), build script changes
• threejs (r80 → r80.p0), build script changes
• 🤔 widgetsnbextension (3.1.1 → 3.2.0)

Optional SPKGs that have changed.

☺: Proper support for optional packages is finally possible. But let's do this as part of another issue.

Experimental SPKGs that have changed.

☺: Proper support for experimental packages is finally possible. But let's do this as part of another issue.

New runtime dependencies:

The dependencies of the sagelib target have not changed upstream, so all new packages should be runtime dependencies in the sage package.

• packaging (17.1)

New build-time dependencies:

The dependencies of the sagelib target have not changed upstream, so there should be no new build-time dependencies.

Build on osx

• Patch cython for cython/cython#466
• Use code from https://trac.sagemath.org/ticket/22554

Update to 8.8.rc1

Changes to sagelib

• Remove cephes, libgap. Add gap, gmpy2, libbraiding, libhomfly, pplpy

Updates to packages

• Update gmpy2 to the new beta. (conda-forge/gmpy2-feedstock#14)
• Package pplpy (conda-forge/staged-recipes#8566)
• Package libbraiding (conda-forge/staged-recipes#8580)
• Package libhomfly (conda-forge/staged-recipes#8576)
• Update gap to 4.10.1 (conda-forge/gap-feedstock#16)
• Update brial to 1.2.5 (conda-forge/brial-feedstock#13)
• Update cddlib to 0.94j
• Update eclib to 20190226 (conda-forge/eclib-feedstock#12)
• Update giac to 1.5.0.37 (conda-forge/giac-feedstock#9)
• Update gsl to 2.5 (conda-forge/gsl-feedstock#44)
• Update giac for gsl 2.5
• Update fflas-ffpack for gsl 2.5
• Update cvxopt for gsl 2.5
• Update maxima to 5.42.2 (conda-forge/maxima-feedstock#16)
• Update pari to 2.11.1 (conda-forge/pari-feedstock#18)
• Update lcalc for pari 2.11
• Update giac for pari 2.11
• Update eclib for pari 2.11
• Update cypari2 for pari 2.11
• Update cysignals for pari 2.11
• Update pynac to 0.7.24 (conda-forge/pynac-feedstock#15)
• Update singular to 4.1.1 (conda-forge/singular-feedstock#5)
• Update pynac for singular 4.1.1
• Update zn_poly to 0.9.1 (conda-forge/zn_poly-feedstock#4)
• Update eclib for ntl 11.3.2
• Update linbox for ntl 11.3.2
• Update flint for ntl 11.3.2
• Update singular for ntl 11.3.2
• Update ecl for bdw-gc 8 (conda-forge/ecl-feedstock#12)

Not sure whether these versions are needed

• Update igraph to 0.7.1999
• Update python_igraph to 0.7.19999

Not important

• Update pkgconfig to 1.4.0
• Update gfan for singular 4.1.1

Sage standard packages not yet packaged

Docs

• thebe

Sagenb

• flask_autoindex
• flask_oldsessions
• flask_silk
• jmol (conda-forge/staged-recipes#5996)
• mathjax
• sagenb
• sagenb_export

Other

• sagetex

Conda Sage launch fails with error No Cython module found

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

After installing sage per the exact instructions on this page: https://doc.sagemath.org/html/en/installation/conda.html#sec-installation-conda
Running sage leads to an immediate crash
Python version is 3.9

Stack backtrace

Could not attach to process. If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user. For more details, see /etc/sysctl.d/10-ptrace.conf
ptrace: Inappropriate ioctl for device.
No stack.
Traceback (most recent call last):
File "", line 25, in
ModuleNotFoundError: No module named 'Cython'
Error while executing Python code.
warning: Inferior ID 1 is not running.
Saved trace to /home/cenobyte/.sage/crash_logs/crash_l8jzlsxk.log

Unhandled SIGILL: An illegal instruction occurred.
This probably occurred because a compiled module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.

Illegal instruction (core dumped)
(sage) cenobyte@Riemann:~$

Installed packages

# packages in environment at /home/cenobyte/mambaforge:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
brotli-python             1.0.9           py310hd8f1fbe_9    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.19.1               hd590300_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     23.1.0          py310hff52083_0    conda-forge
conda-package-handling    2.0.2              pyh38be061_0    conda-forge
conda-package-streaming   0.8.0              pyhd8ed1ab_0    conda-forge
cryptography              41.0.2          py310h75e40e8_0    conda-forge
fmt                       9.1.0                h924138e_0    conda-forge
icu                       72.1                 hcb278e6_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.1               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libarchive                3.6.2                h039dbb9_1    conda-forge
libcurl                   8.1.2                hca28451_1    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libmamba                  1.4.2                hcea66bb_0    conda-forge
libmambapy                1.4.2           py310h1428755_0    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libsolv                   0.7.24               hfc55251_1    conda-forge
libsqlite                 3.42.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxml2                   2.11.4               h0d562d8_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.4.2           py310h51d5547_0    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
pluggy                    1.2.0              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4           py310h5764c6d_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.12         hd12c33a_0_cpython    conda-forge
python_abi                3.10                    3_cp310    conda-forge
readline                  8.2                  h8228510_1    conda-forge
reproc                    14.2.4               h0b41bf4_0    conda-forge
reproc-cpp                14.2.4               hcb278e6_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.32         py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.7           py310h1fa729e_1    conda-forge
setuptools                68.0.0             pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   2.0.3              pyhd8ed1ab_1    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
zstandard                 0.19.0          py310h1275a96_2    conda-forge
zstd                      1.5.2                hfc55251_7    conda-forge

Environment info

conda info

     active environment : None
            shell level : 0
       user config file : /home/cenobyte/.condarc
 populated config files : /home/cenobyte/mambaforge/.condarc
                          /home/cenobyte/.condarc
          conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.12.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=5.19.0=0
                          __unix=0=0
       base environment : /home/cenobyte/mambaforge  (writable)
      conda av data dir : /home/cenobyte/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/cenobyte/mambaforge/pkgs
                          /home/cenobyte/.conda/pkgs
       envs directories : /home/cenobyte/mambaforge/envs
                          /home/cenobyte/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.31.0 CPython/3.10.12 Linux/5.19.0-50-generic ubuntu/22.04.2 glibc/2.35
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

dependency conflict with jupyterhub-base (old tornado?)

Issue:

Hello! I am trying to install sagemath with conda on the docker images for our local jupyterhub.
This docker image is based on the jupyter/base-notebook image from Jupyter's Core stack.
The latter includes the jupyterhub conda package which itself depends on jupyterhub-base.

There is however a conflict with this package and sage which I could reduce to the following.
Note: I am using mamba rather than conda because it's faster and the error messages are more explicit, but the failure occurs also with conda:

mamba create -n sage sage jupyterhub-base -c conda-forge
Encountered problems while solving.
Problem: nothing provides path.py >=7.1,<8 needed by sage-8.1-py27_1

Trying to force python 3.7 did not help:

mamba create -n sage sage=9.1=py37hc8dfbb8_0 jupyterhub-base -c conda-forge
Problem: package sage-9.1-py37hc8dfbb8_0 requires python_abi 3.7.* *_cp37m, but none of the providers can be installed

At some point in my various trials, the messages seemed to suggest that sage requested tornado < 5.0 when jupyterhub required a more recent tornado.

Thanks in advance!

Environment (conda list):
(base) debian@geops:~$ conda list

``` $ conda list # packages in environment at /home/debian/miniconda3: # # Name Version Build Channel _libgcc_mutex 0.1 main bzip2 1.0.8 h516909a_2 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge certifi 2020.6.20 py37hc8dfbb8_0 conda-forge cffi 1.14.0 py37h2e261b9_0 chardet 3.0.4 py37_1003 conda 4.8.3 py37hc8dfbb8_1 conda-forge conda-package-handling 1.6.1 py37h7b6447c_0 cryptography 2.9.2 py37h1ba5d50_0 icu 67.1 he1b5a44_0 conda-forge idna 2.9 py_1 krb5 1.17.1 h173b8e3_0 ld_impl_linux-64 2.33.1 h53a641e_7 libarchive 3.3.3 h3a8160c_1008 conda-forge libcurl 7.71.1 hcdd3856_3 conda-forge libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 9.1.0 hdf63c60_0 libiconv 1.15 h516909a_1006 conda-forge libsolv 0.7.14 h8b12597_3 conda-forge libssh2 1.9.0 hab1572f_4 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 libxml2 2.9.10 h72b56ed_1 conda-forge lz4-c 1.9.2 he1b5a44_1 conda-forge lzo 2.10 h14c3975_1000 conda-forge mamba 0.4.2 py37h6d3251c_0 conda-forge ncurses 6.2 he6710b0_1 openssl 1.1.1g h516909a_0 conda-forge pip 20.0.2 py37_3 pycosat 0.6.3 py37h7b6447c_0 pycparser 2.20 py_0 pyopenssl 19.1.0 py37_0 pysocks 1.7.1 py37_0 python 3.7.7 h191fe78_0_cpython python_abi 3.7 1_cp37m conda-forge readline 7.0 h7b6447c_5 requests 2.23.0 py37_0 ruamel_yaml 0.15.87 py37h7b6447c_0 setuptools 46.4.0 py37_0 six 1.14.0 py37_0 sqlite 3.31.1 h62c20be_1 tk 8.6.8 hbc83047_0 tqdm 4.46.0 py_0 urllib3 1.25.8 py37_0 wheel 0.34.2 py37_0 xz 5.2.5 h7b6447c_0 yaml 0.1.7 had09818_2 zlib 1.2.11 h7b6447c_3 zstd 1.4.5 h6597ccf_1 conda-forge ```

Details about conda and system ( conda info ):

``` $ conda info active environment : base active env location : /home/debian/miniconda3 shell level : 1 user config file : /home/debian/.condarc populated config files : conda version : 4.8.3 conda-build version : not installed python version : 3.7.7.final.0 virtual packages : __glibc=2.24 base environment : /home/debian/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 package cache : /home/debian/miniconda3/pkgs /home/debian/.conda/pkgs envs directories : /home/debian/miniconda3/envs /home/debian/.conda/envs platform : linux-64 user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.7 Linux/4.9.0-6-amd64 debian/9.4 glibc/2.24 UID:GID : 1000:1000 netrc file : None offline mode : False

</details>

Search for documentation with ? segfaults in ipython

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

The ? operator seems to reliably cause a segfault in SageMath 9.7 from conda.

This happens in a freshly created environment with mamba create -n sage97 sage=9.7.

(sage97) ~/p/e/sage-flatsurf $ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.7, Release Date: 2022-09-19                     │
│ Using Python 3.10.8. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
sage: numerical_approx?
------------------------------------------------------------------------
/home/jule/proj/umamba/envs/sage97/lib/python3.10/site-packages/cysignals/signals.cpython-310-x86_64-linux-gnu.so(+0x6f4d)[0x7fa7c47f5f4d]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/site-packages/cysignals/signals.cpython-310-x86_64-linux-gnu.so(+0x714c)[0x7fa7c47f614c]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/site-packages/cysignals/signals.cpython-310-x86_64-linux-gnu.so(+0x972c)[0x7fa7c47f872c]
/usr/lib/libc.so.6(+0x38a00)[0x7fa7c517ca00]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/lib-dynload/../../libncursesw.so.6(termattrs_sp+0x2f)[0x7fa76e7b5b9f]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/lib-dynload/../../libncursesw.so.6(+0x1dea5)[0x7fa76e7b2ea5]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/lib-dynload/../../libncursesw.so.6(newterm_sp+0xbf)[0x7fa76e7ae5ef]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/lib-dynload/../../libncursesw.so.6(newterm+0x3b)[0x7fa76e7aeaab]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/lib-dynload/../../libncursesw.so.6(initscr+0x73)[0x7fa76e7aabf3]
/home/jule/proj/umamba/envs/sage97/lib/python3.10/lib-dynload/_curses.cpython-310-x86_64-linux-gnu.so(+0x1187e)[0x7fa76e7e287e]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1417a3)[0x55a0e32917a3]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x4a35)[0x55a0e3287e55]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x4a35)[0x55a0e3287e55]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x304)[0x55a0e3283724]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x304)[0x55a0e3283724]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x4a35)[0x55a0e3287e55]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x150d7c)[0x55a0e32a0d7c]
/home/jule/proj/umamba/envs/sage97/bin/python(PyObject_Call+0xb8)[0x55a0e32a1a08]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x2b8f)[0x55a0e3285faf]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x150d7c)[0x55a0e32a0d7c]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x12ff)[0x55a0e328471f]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x151002)[0x55a0e32a1002]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x2b8f)[0x55a0e3285faf]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x6f3)[0x55a0e3283b13]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1e64d2)[0x55a0e33364d2]
/home/jule/proj/umamba/envs/sage97/bin/python(PyEval_EvalCode+0x87)[0x55a0e3336417]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1edb4f)[0x55a0e333db4f]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x144231)[0x55a0e3294231]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x304)[0x55a0e3283724]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1f026d)[0x55a0e334026d]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x1ad0)[0x55a0e3284ef0]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1f026d)[0x55a0e334026d]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x1ad0)[0x55a0e3284ef0]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1f026d)[0x55a0e334026d]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x205d99)[0x55a0e3355d99]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x14fb31)[0x55a0e329fb31]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x6f3)[0x55a0e3283b13]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x304)[0x55a0e3283724]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x6f3)[0x55a0e3283b13]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x150d7c)[0x55a0e32a0d7c]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x12ff)[0x55a0e328471f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x6f3)[0x55a0e3283b13]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x6f3)[0x55a0e3283b13]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyFunction_Vectorcall+0x6f)[0x55a0e329403f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyEval_EvalFrameDefault+0x6f3)[0x55a0e3283b13]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1e64d2)[0x55a0e33364d2]
/home/jule/proj/umamba/envs/sage97/bin/python(PyEval_EvalCode+0x87)[0x55a0e3336417]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x219ed9)[0x55a0e3369ed9]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x2147e4)[0x55a0e33647e4]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x98214)[0x55a0e31e8214]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyRun_SimpleFileObject+0x1af)[0x55a0e335eb1f]
/home/jule/proj/umamba/envs/sage97/bin/python(_PyRun_AnyFileObject+0x43)[0x55a0e335e6e3]
/home/jule/proj/umamba/envs/sage97/bin/python(Py_RunMain+0x39f)[0x55a0e335b89f]
/home/jule/proj/umamba/envs/sage97/bin/python(Py_BytesMain+0x39)[0x55a0e3329709]
/usr/lib/libc.so.6(+0x23290)[0x7fa7c5167290]
/usr/lib/libc.so.6(__libc_start_main+0x8a)[0x7fa7c516734a]
/home/jule/proj/umamba/envs/sage97/bin/python(+0x1d9611)[0x55a0e3329611]
------------------------------------------------------------------------
Attaching gdb to process id 132865.
Cannot find gdb installed
GDB is not installed.
Install gdb for enhanced tracebacks.
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------
[1]    132865 segmentation fault (core dumped)  sage

Installed packages

_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
alsa-lib                  1.2.8                h166bdaf_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
arb                       2.23.0               h44d021b_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_3    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
babel                     2.11.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bdw-gc                    8.0.6                h4bd325d_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
beniget                   0.4.1              pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.39                 he00db2b_1    conda-forge
binutils_linux-64         2.39                h5fc0e48_11    conda-forge
blas-devel                3.9.0           16_linux64_openblas    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
brial                     1.2.12             pyha3edaa6_0    conda-forge
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1005    conda-forge
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
cddlib                    1!0.94m              h9202a9a_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
cliquer                   1.22                 h36c2ea0_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7           py310hdf3cbec_0    conda-forge
cryptography              39.0.0          py310h34c0648_0    conda-forge
curl                      7.86.0               h2283fc2_1    conda-forge
cvxopt                    1.3.0           py310hdd05ad1_4    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cypari2                   2.1.3           py310h75a4d73_0    conda-forge
cysignals                 1.11.2          py310h15010d2_0    conda-forge
cython                    0.29.33         py310heca2aa9_0    conda-forge
debugpy                   1.6.5           py310heca2aa9_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.17.1          py310hff52083_3    conda-forge
dsdp                      5.8               hd9d9efa_1203    conda-forge
ecl                       21.2.1               h9d73b02_2    conda-forge
eclib                     20220621             h87840bb_1    conda-forge
ecm                       7.0.4             h9202a9a_1002    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h27087fc_0    conda-forge
fflas-ffpack              2.4.3                h912ac81_2    conda-forge
fftw                      3.3.10          nompi_hf0379b8_106    conda-forge
flintqs                   1.0               h85f3911_1001    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.1               hc2a2eb6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0          py310h5764c6d_1    conda-forge
fplll                     5.4.2                hbb93ad8_1    conda-forge
fpylll                    0.5.7           py310h3ca1b1e_1    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gap-core                  4.11.1               hd225dc4_4    conda-forge
gap-defaults              4.11.1               ha770c72_4    conda-forge
gast                      0.5.3              pyhd8ed1ab_0    conda-forge
gcc_impl_linux-64         10.4.0              h5231bdf_19    conda-forge
gcc_linux-64              10.4.0              h9215b83_11    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gf2x                      1.3.0                ha476b99_2    conda-forge
gfan                      0.6.2             hb86e20a_1003    conda-forge
gfortran_impl_linux-64    10.4.0              h7d168d2_19    conda-forge
giac                      1.9.0.21             he9ede01_0    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
givaro                    4.1.1                h192cbe9_1    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.2           py310h3ec546c_1    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gxx_impl_linux-64         10.4.0              h5231bdf_19    conda-forge
gxx_linux-64              10.4.0              h6e491c6_11    conda-forge
harfbuzz                  6.0.0                h8e241bc_0    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
igraph                    0.9.10               ha1f048c_1    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
iml                       1.0.5             hd75c201_1003    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib_resources       5.10.2             pyhd8ed1ab_0    conda-forge
ipykernel                 6.20.2             pyh210e3f2_0    conda-forge
ipython                   8.8.0              pyh41d4057_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.7.2              pyhd8ed1ab_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jmol                      14.32.10             ha770c72_0    conda-forge
jpeg                      9e                   h166bdaf_2    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_core              4.12.0          py310hff52083_0    conda-forge
jupyter_server            1.23.5             pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.1              pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4           py310hbf28c38_1    conda-forge
krb5                      1.19.3               h08a2579_0    conda-forge
lcalc                     2.0.5                h8cd7e2e_0    conda-forge
lcms2                     2.14                 h6ed2654_0    conda-forge
ld_impl_linux-64          2.39                 hcc3a1bd_1    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbraiding               1.1                  h58526e2_0    conda-forge
libbrial                  1.2.12               h138cd66_0    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcups                   2.3.3                h3e49a29_2    conda-forge
libcurl                   7.86.0               h2283fc2_1    conda-forge
libdeflate                1.14                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflint                  2.9.0           h2f819a4_ntl_100    conda-forge
libgcc-devel_linux-64     10.4.0              hd38fd1e_19    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgd                     2.3.3                h18fbbfe_3    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglib                   2.74.1               h606061b_1    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libhomfly                 1.02r6               h36c2ea0_0    conda-forge
libhwloc                  2.8.0                h32351e8_1    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
liblapacke                3.9.0           16_linux64_openblas    conda-forge
libnghttp2                1.51.0               hff17c54_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsanitizer              10.4.0              h5246dfb_19    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.40.0               h753d276_0    conda-forge
libssh2                   1.10.0               hf14f497_3    conda-forge
libstdcxx-devel_linux-64  10.4.0              hd38fd1e_19    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.4.0                h82bc61c_5    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.4                h522a892_0    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.10.3               h7463322_0    conda-forge
libxslt                   1.1.37               h873f0b0_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
linbox                    1.6.3                h9d78c56_7    conda-forge
lrcalc                    2.1                  h27087fc_4    conda-forge
lxml                      4.9.2           py310hbdc0903_0    conda-forge
m4ri                      20140914          h7ca028e_1005    conda-forge
m4rie                     20150908          h7ca028e_1001    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
markupsafe                2.1.2           py310h1fa729e_0    conda-forge
matplotlib-base           3.6.3           py310he60537e_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
maxima                    5.45.0               h9d73b02_3    conda-forge
memory-allocator          0.1.2           py310h5764c6d_2    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mistune                   0.8.4           pyh1a96a4e_1006    conda-forge
mpc                       1.2.1                h9f54685_0    conda-forge
mpfi                      1.5.4             h9f54685_1001    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nauty                     2.7.2                h7f98852_0    conda-forge
nbclassic                 0.4.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.6.8              pyhd8ed1ab_0    conda-forge
nbconvert                 6.5.3              pyhd8ed1ab_0    conda-forge
nbconvert-core            6.5.3              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          6.5.3              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  2.8.8              pyhd8ed1ab_0    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
ntl                       11.4.3               hef3c4d3_1    conda-forge
numpy                     1.24.1          py310h08bbf29_0    conda-forge
openblas                  0.3.21          pthreads_h320a7e8_3    conda-forge
openjdk                   17.0.3               h58dac75_5    conda-forge
openjpeg                  2.5.0                h7d73246_1    conda-forge
openssl                   3.0.7                h0b41bf4_1    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
palp                      2.20                 h36c2ea0_0    conda-forge
pandoc                    2.19.2               h32600fe_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.12              hd33c08f_1    conda-forge
pari                      2.13.3          he2feae2_1_pthread    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.2.0           py310h454ad03_3    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkg-config                0.29.2            h36c2ea0_1008    conda-forge
pkgconfig                 1.5.5              pyhd8ed1ab_4    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
planarity                 3.0.0.5           h36c2ea0_1002    conda-forge
ply                       3.11                       py_1    conda-forge
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
ppl                       1.2               h6ec01c2_1006    conda-forge
pplpy                     0.8.6           py310he9160dc_1    conda-forge
primecount                7.4                  hcb278e6_1    conda-forge
primecountpy              0.1.0           py310hbf28c38_2    conda-forge
primesieve                8.0                  h27087fc_0    conda-forge
prometheus_client         0.15.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
psutil                    5.9.4           py310h5764c6d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py310h1fa729e_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.8          h4a9ceb5_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-lrcalc             2.1             py310hd8f1fbe_4    conda-forge
python-tzdata             2022.7             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pythran                   0.11.0          py310hc4a4660_3    conda-forge
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pytz-deprecation-shim     0.1.0.post0     py310hff52083_3    conda-forge
pyzmq                     23.2.1          py310h330234f_0    conda-forge
qd                        2.3.22            h2cc385e_1004    conda-forge
r-base                    4.2.2                hb87df5d_1    conda-forge
ratpoints                 2.1.3             h445213a_1002    conda-forge
readline                  8.1.2                h0f457ee_0    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
rpy2                      3.5.7           py310r42h0a54255_0    conda-forge
rubiks                    20070912          h58526e2_1001    conda-forge
rw                        0.9                  h7f98852_0    conda-forge
sage                      9.7                  hd8ed1ab_0    conda-forge
sage-docbuild             9.7                      pypi_0    pypi
sage-setup                9.7                      pypi_0    pypi
sagelib                   9.7             py310h28be7dd_1    conda-forge
sagemath-db-combinatorial-designs 20140630                      1    conda-forge
sagemath-db-conway-polynomials 0.5.0                ha878542_1    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20210214             hd8ed1ab_0    conda-forge
sagemath-db-polytopes     20170220                      1    conda-forge
sagemath-standard         9.7                      pypi_0    pypi
sagetex                   3.6.1              pyhd8ed1ab_0    conda-forge
scipy                     1.10.0          py310h8deb116_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                66.1.0             pyhd8ed1ab_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singular                  4.2.1.p3             hb16e69e_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sphinx                    4.5.0              pyh6c4a22f_0    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlite                    3.40.0               h4ff8645_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
suitesparse               5.10.1               h9e50725_1    conda-forge
symmetrica                2.0               h58526e2_1007    conda-forge
sympow                    2.023.6              h779893b_2    conda-forge
sympy                     1.11.1          py310hff52083_2    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tachyon                   0.99b6            h794f8fd_1001    conda-forge
tbb                       2021.7.0             h924138e_1    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
three.js                  122                  hd8ed1ab_2    conda-forge
threejs-sage              122                  hd8ed1ab_2    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
tornado                   6.2             py310h5764c6d_1    conda-forge
traitlets                 5.8.1              pyhd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022g                h191b570_0    conda-forge
tzlocal                   4.2             py310hff52083_2    conda-forge
unicodedata2              15.0.0          py310h5764c6d_0    conda-forge
urllib3                   1.26.14            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.4.2              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.1              pyha770c72_0    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-inputproto           2.3.2             h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h7f98852_0    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-libxtst              1.2.3             h7f98852_1002    conda-forge
xorg-recordproto          1.14.2            h7f98852_1002    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xsimd                     8.0.5                h4bd325d_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.11.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zn_poly                   0.9.2                h9202a9a_0    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Environment info

active environment : sage97
    active env location : /home/jule/proj/umamba/envs/sage97
            shell level : 2
       user config file : /home/jule/.condarc
 populated config files : /home/jule/.condarc
          conda version : 22.11.1
    conda-build version : not installed
         python version : 3.9.15.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.36=0
                          __linux=6.1.4=0
                          __unix=0=0
       base environment : /home/jule/proj/umamba  (writable)
      conda av data dir : /home/jule/proj/umamba/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          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
          package cache : /home/jule/proj/umamba/pkgs
                          /home/jule/.conda/pkgs
       envs directories : /home/jule/proj/umamba/envs
                          /home/jule/.conda/envs
               platform : linux-64
             user-agent : conda/22.11.1 requests/2.28.1 CPython/3.9.15 Linux/6.1.4-arch1-1 arch/rolling glibc/2.36
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Segfault when computing resultant

The following code:

Rx = PolynomialRing(RationalField(), 'x')
R = PolynomialRing(Rx, 'y')
R('-y^2 + x^2 - x + 1').resultant(R('(2*x - 1)*y'))

results in a segfault in

> * thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT
>   * frame #0: 0x00007fff203b84c2 libsystem_kernel.dylib`__kill + 10
>     frame #1: 0x000000010ffd40ac libpari-gmp-tls.dylib`pari_err + 4940
>     frame #2: 0x000000010fca26ec libpari-gmp-tls.dylib`_gtopoly + 172
>     frame #3: 0x00000001169ec422 gen.cpython-39-darwin.so`__pyx_pf_7cypari2_3gen_8Gen_base_14Polrev + 178
>     frame #4: 0x000000010f7b450c signals.cpython-39-darwin.so`__Pyx_CyFunction_CallAsMethod + 92
>     frame #5: 0x0000000118534c77 polynomial_element.cpython-39-darwin.so`__Pyx_PyObject_Call2Args + 215
>     frame #6: 0x00000001185972cf polynomial_element.cpython-39-darwin.so`__pyx_pw_4sage_5rings_10polynomial_18polynomial_element_10Polynomial_221_pari_with_name + 1071
>     frame #7: 0x000000010f0b1f24 python`cfunction_call + 52
>     frame #8: 0x0000000118534ea3 polynomial_element.cpython-39-darwin.so`__Pyx_PyObject_CallOneArg + 339
>     frame #9: 0x00000001185967a2 polynomial_element.cpython-39-darwin.so`__pyx_pw_4sage_5rings_10polynomial_18polynomial_element_10Polynomial_217__pari__ + 386
>     frame #10: 0x0000000118535904 polynomial_element.cpython-39-darwin.so`__Pyx_PyObject_CallNoArg + 132
>     frame #11: 0x0000000118598497 polynomial_element.cpython-39-darwin.so`__pyx_pw_4sage_5rings_10polynomial_18polynomial_element_10Polynomial_231resultant + 551
>     frame #12: 0x000000010f060bd5 python`method_vectorcall_O + 117
>     frame #13: 0x00000001108491d4 element.cpython-39-darwin.so`__pyx_pw_4sage_9structure_7element_12coerce_binop_1new_method + 1208
>     frame #14: 0x000000010f051288 python`_PyObject_MakeTpCall + 136
>     frame #15: 0x000000010f055d9e python`method_vectorcall + 686
>     frame #16: 0x000000010f186e4f python`call_function + 175
> 

with SageMath-9.3 and pari 2.13.2-h491590d_1_pthread but works fine with pari 2.11.4-h797e938_2 using python 3.9.9 on Mac OS 11.5.2 x86_64. Note that this also failed in my conda environment with SageMath-9.4, but worked fine with the one with SageMath-9.2.

More precisely: I get the crash when creating a conda environment with SageMath-9.3. I can then fix the crash or re-create the crash by changing with conda environment with "conda install pari==2.11.4" or "conda install 2.13.2".

Those commands change the packages as follows:

added / updated specs:
- pari==2.11.4

The following packages will be DOWNGRADED:

cypari2 2.1.2-py39hbeebeb8_3 --> 2.1.2-py39he58a9ab_0
cysignals 1.11.2-py39h7972417_0 --> 1.10.3-py39h520947a_0
eclib 20210503-h06317ce_2 --> 20210503-h5af3530_0
giac 1.6.0.47-h3e19eb6_2 --> 1.6.0.47-h5514456_0
lcalc 1.23-he3dd645_1006 --> 1.23-h3e22c04_1004
pari 2.13.2-h491590d_1_pthread --> 2.11.4-h797e938_2
sagelib 9.3-py39hf07016b_5 --> 9.3-py39h2a6771f_4

l also tried Marc Culler's Sage releases (https://github.com/3-manifolds/Sage_macOS/releases), version 9.4 and 9.5 prerelease. The crash didn't happen in either version. I think those use pari 2.13.1 and 2.13.3.

Hmmm... I noted that the downgrading that fixed the crash removed "_pthread" from the pari version. So maybe pthread support causes the crash.

Update to 8.0

8.0.beta3 is out, so it seems like we need to update a few packages.

• Update sagemath-db-conway-polynomials to 0.5
• Update cysignals to 1.6.3
• Update pari to 2.9.2

Also need to package cypari2

Upgrade to 8.2

The list of packages has been compiled with git diff 8.1..8.2.rc4 build/.

TODO: Update this list with any SPKG changes that happen from 8.2.rc4 to 8.2.

🤔: These packages are probably not the right version in conda-forge but they should not matter for the conda release.

Base SPKGs that have changed.

none.

Standard SPKGs that have changed.

• alabaster (0.7.8.p0 → 0.7.10), no patch changes
• arb (2.11.1.p0 → 2.12.0.p0), no patch changes; conda-forge/arb-feedstock#7
• babel (2.3.4.p0 → 2.5.1), no patch changes
• BRiAl (1.0.1.p1 → 1.0.1.p2), upgrades Sage's own build system
• backports.functools.lru_cache (× → 1.4)
• bleach (× → 2.1.3)
• bzip2 (1.0.6-20150304 → 1.0.6-20150304.p0)
• cddlib (094g.p1 → 094g.p2), build script changes
• certifi (2016.2.28.p0 → 2017.11.5)
• cliquer (1.21.p3 → 1.21.p4), build scirpt changes
• configure (247 → 261)
• cypari (1.1.3 → 1.1.4)
• cysignals (1.6.5 → 1.7.0.p0), added stack_guard.patch
• cython (0.27.2 → 0.28.1)
• docutils (0.13.1 → 0.14)
• ecl (16.1.2.p4 → 16.1.2.p5), only changes to build system
• eclib (20171002 → 20171002.p0), only changes to build system
• ecm (7.0.4.p0 → 7.0.4.p1), only changes to build system
• entrypoints (0.2.2 → 0.2.3)
• fflas_ffpack (2.2.2.p0 → 2.3.2), drops ticket-21578.patch
• flint (2.5.2.p1 → 2.5.2.p2), patch for FreeBSD added.
• flintqs (1.0 → 1.0.p0), only build system changes
• fplll (5.2.0 → 5.2.0.p1), patch for Solaris (and nobody else I hope)
• freetype (2.6.3 → 2.8.1)
• future (0.15.2.p0 → 0.16.0)
• gc (7.2f.p1 → 7.6.4)
• gf2x (1.2 → 1.2.p0), only build system changes
• giac (1.2.3.47.p0 → 1.4.9.45.p2), drops cSolveorder-check.patch, libpng16.patch, adds dirent.patch, alloca.patch, sunos_abs.patch
• givaro (4.0.2.p0 → 4.0.4)
• glpk (4.63.p1 → 4.63.p2), just build system changes
• gsl (2.3 → 2.3.p0), just build system changes
• html5lib (× → 1.0.1)
• iconv (1.14 → 1.15)
• iml (1.0.4p1.p1 → 1.0.4p1.p2), just build system changes
• ipykernel (4.6.1 → 4.7.0)
• 🤔 ipython (5.1.0 → 5.5.0), conda packages version 6, not 5.
• ipywidgets (6.0.0 → 7.1.1)
• jinja2 (2.8.p0 → 2.10)
• 🤔 jmol (14.6.1_2016.07.11.p0 → 14.6.1_2016.07.11.p1), we did not have that one packaged before either
• jsonschema (2.5.1.p0 → 2.6.0)
• jupyter_client (5.1.0 → 5.2.2)
• jupyter_core (4.3.0 → 4.4.0)
• lcalc (1.23.p15 → 1.23.p16), adds pari-mem.patch, seems to be only relevant for cygwin.
• libatomic_ops (× → 7.6.2)
• libgap (4.8.6 → 4.8.6.p0), only build system changes
• libgd (2.1.1.1.p0 → 2.1.1.1.p1), only build system changes
• libpng (1.6.29 → 1.6.29.p0), only build system changes
• linbox (1.4.2.p1 → 1.5.2), lots of patch changes
• lrcalc (1.2.p0 → 1.2.p1), only build system changes
• m4ri (20140914 → 20140914.p0), only build system changes
• m4rie (20150908 → 20150908.p0), only build system changes
• markupsafe (0.23.p0 → 1.0)
• mpfi (1.5.1 → 1.5.2)
• mpc (1.0.3.p0 → 1.1.0), drop mpc_mul_faster.patch
• mpfr (3.1.5.p0 → 4.0.1), drop clang_workaround.patch
• mpmath (0.19.p0 → 1.0.0)
• 🤔 nbconvert (4.2.0.p0 → 5.3.1)
• ncurses (6.0 → 6.0.p0)
• 🤔 notebook (4.4.1.p0 → 5.3.1), we had not packaged the notebook before and sage worked without.
• numpy (1.13.3.p0 → 1.13.3.p1), build system changes
• pandocfilters (1.3.0 → 1.4.2), upgraded to standard
• pathlib2 (2.1.0.p0 → 2.3.0)
• pcre (8.40.p0 → 8.40.p2), build system changes only
• pickleshare (0.7.2.p0 → 0.7.4)
• pillow (3.3.0 → 4.3.0), currently conda is on a different major version but 4.3.0 was packaged here conda-forge/pillow-feedstock@e93af41#diff-e178b687b10a71a3348107ae3154e44c
• pip (9.0.1 → 9.0.3)
• pkgconf (0.9.7 → 0.9.7.p0), build system changes only
• planarity (3.0.0.5 → 3.0.0.5.p0), build system changes only
• ppl (1.2 → 1.2.p1), added clang5-support.patch
• prompt_toolkit (1.0.9 → 1.0.15)
• psutil (5.2.0.p0 → 5.2.0.p1), only changes to cygwin patches
• pynac (0.7.12 → 0.7.16.p0), added memleak.patch
• pyparsing (2.1.5.p0 → 2.2.0)
• pytz (2016.4.p0 → 2017.3)
• 🤔 pyzmq (16.0.0 → 17.0.0b3)
• 🤔 r (3.4.2.p0 → 3.4.3.p0), we still have 3.4.1 in conda, let's see if that is good enough
• readline (6.3.008 → 6.3.008.p0), conda has 7.0
• rw (0.7 → 0.7.p0)
• scandir (× → 1.6)
• send2trash (× → 1.4.2)
• setuptools (33.1.1 → 38.2.4.p0), build system changes
• setuptools_scm (1.11.1.p0 → 1.15.6)
• 🤔 singular (4.1.0p3.p0 → 4.1.0p3.p2), adds a few patches
• sphinxcontrib_websupport (× → 1.0.1)
• sqlite (autoconf-3170000 → 3220000)
• subprocess32 (× → 3.2.7.p0), adds fix_config.py which seems to be relevant for Solaris only
• 🤔 sympy (1.1.1 → 1.1.1.p0), adds prec-to-precision-in-core-numbers.patch
• terminado (0.6 → 0.8.1)
• testpath (× → 0.3.1)
• tornado (4.3.p0 → 4.5.2), conda has version 5 but that should be fine
• traitlets (4.3.1 → 4.3.2)
• typing (3.6.1 → 3.6.2)
• webencodings (× → 0.5.1)
• widgetsnbextension (2.0.0 → 3.1.1)
• xz (5.2.2 → 5.2.2.p0)
• yasm (1.3.0 → 1.3.0.p0), build system changes only
• zeromq (4.0.5.p1 → 4.0.5.p2), build system changes only
• zope_interface (4.2.0.p0 → 4.4.3), where is this package in conda-forge?

Optional SPKGs that have changed.

😞: Proper support for optional packages won't come before Sage 8.3 with the inclusion of https://trac.sagemath.org/ticket/20382. These packages are probably not present in conda-forge but it does not matter at the moment as they would not be detected by Sage anyway.

• ccache (3.2.2 → 3.3.4)
• coxeter3 (1.1 → 8ac9c71723c8ca57a836d6381aed125261e44e9e)
• gambit (15.1.1 → 15.1.1.p0)
• gmpy2 (2.0.8.p0 → 2.1.0a1.p1)
• libhomfly (1.0r2 → 1.02r4)
• meataxe (2.4.24.p3 → 1.0)
• matplotlib (1.5.1.p0 → 2.1.0)
• maxima (5.39.0.p0 → 5.39.0.p2), only build system changes
• mistune (0.7.3.p0 → 0.8.3)
• notedown (dfda648b → 1.5.1)
• openssl (1.0.2m → 1.1.0h)
• pari_jupyter (1.2.2 → 1.3.2)
• qhull (2015-src-7.2.0 → 2015-src-7.2.0.p1)
• singular_jupyter (0.9.2 → 0.9.7)

Experimental SPKGs that have changed.

😞: Similarly as for optional SPKGs we don't really care yet.
none.

New runtime dependencies:

The dependencies of the sagelib target have not changed upstream, so all new packages should be runtime dependencies in the sage package.

• backports.functools.lru_cache (× → 1.4)
• libatomic_ops (× → 7.6.2)
• scandir (× → 1.6)
• send2trash (× → 1.4.2)
• sphinxcontrib_websupport (× → 1.0.1)
• subprocess32 (× → 3.2.7.p0)

New build-time dependencies:

The dependencies of the sagelib target have not changed upstream, so there should be no new build-time dependencies.

installing sage from conda-forge

Issue:
unable to install sage; I created a new environment and then:

source activate MySageEnv
conda install -c conda-foge sage

it gives me several errors, e.g.,:

CondaVerificationError: The package for sympy located at /home/wyousef/Downloads/AAProgramsAA/anaconda3/pkgs/sympy-1.3-py27_1000
appears to be corrupted. The path 'lib/python2.7/site-packages/sympy/vector/tests/test_field_functions.pyc'
specified in the package manifest cannot be found.

Details about conda and system ( conda info ):

$ conda info

active environment : None user config file : /home/wyousef/.condarc populated config files : /home/wyousef/.condarc conda version : 4.6.4 conda-build version : not installed python version : 2.7.15.final.0 base environment : /home/wyousef/Downloads/AAProgramsAA/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/wyousef/Downloads/AAProgramsAA/anaconda3/pkgs /home/wyousef/.conda/pkgs envs directories : /home/wyousef/Downloads/AAProgramsAA/anaconda3/envs /home/wyousef/.conda/envs platform : linux-64 user-agent : conda/4.6.4 requests/2.21.0 CPython/2.7.15 Linux/4.20.8-arch1-1-ARCH arch/ glibc/2.28 UID:GID : 1000:1000 netrc file : None offline mode : False

Missing packages

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Following package is not available from conda-forge, which is needed for my work
jupyter_client==7.3.2=pyhd8ed1ab_0

Installed packages

# packages in environment at /home/brotech/mambaforge:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
archspec                  0.2.2              pyhd8ed1ab_0    conda-forge
boltons                   23.1.1             pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.24.0               hd590300_0    conda-forge
ca-certificates           2023.11.17           hbcca054_0    conda-forge
certifi                   2023.11.17         pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py310h2fee648_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     23.11.0         py310hff52083_1    conda-forge
conda-libmamba-solver     23.12.0            pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
distro                    1.8.0              pyhd8ed1ab_0    conda-forge
fmt                       10.1.1               h00ab1b0_1    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py310hff52083_3    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libarchive                3.7.2                h2aa1ff5_1    conda-forge
libcurl                   8.5.0                hca28451_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_3    conda-forge
libgomp                   13.2.0               h807b86a_3    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libmamba                  1.5.6                had39da4_0    conda-forge
libmambapy                1.5.6           py310h39ff949_0    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsolv                   0.7.27               hfc55251_0    conda-forge
libsqlite                 3.44.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxml2                   2.12.3               h232c23b_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.5.6           py310h51d5547_0    conda-forge
menuinst                  2.0.1           py310hff52083_0    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
openssl                   3.2.0                hd590300_1    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pip                       23.3.2             pyhd8ed1ab_0    conda-forge
platformdirs              4.1.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py310h2372a71_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.13         hd12c33a_0_cpython    conda-forge
python_abi                3.10                    4_cp310    conda-forge
readline                  8.2                  h8228510_1    conda-forge
reproc                    14.2.4.post0         hd590300_1    conda-forge
reproc-cpp                14.2.4.post0         h59595ed_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.18.5          py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.7           py310h2372a71_2    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   2.1.0              pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml-cpp                  0.8.0                h59595ed_0    conda-forge
zstandard                 0.22.0          py310h1275a96_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Environment info

active environment : base
    active env location : /home/brotech/mambaforge
            shell level : 1
       user config file : /home/brotech/.condarc
 populated config files : /home/brotech/mambaforge/.condarc
                          /home/brotech/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.10.13.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen3
                          __conda=23.11.0=0
                          __glibc=2.31=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /home/brotech/mambaforge  (writable)
      conda av data dir : /home/brotech/mambaforge/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/brotech/mambaforge/pkgs
                          /home/brotech/.conda/pkgs
       envs directories : /home/brotech/mambaforge/envs
                          /home/brotech/.conda/envs
               platform : linux-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Linux/5.15.0-91-generic ubuntu/20.04.6 glibc/2.31 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.6
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Conda packages for SageMath with Python 3.8

The latest jupyter/xxx-notebook images (e.g. used by binder) are based on Python 3.8.
This seems to be incompatible with the current conda packages:

docker run -ti --user root jupyter/minimal-notebook bash

(base) root@fae0b6c00255:~# conda install mamba -c conda-forge

(base) root@fae0b6c00255:~# mamba install sage
...
Encountered problems while solving.
Problem: nothing provides path.py >=7.1,<8 needed by sage-8.1-py27_1

(base) root@fae0b6c00255:~# mamba install sage=9.1
...
Encountered problems while solving.
Problem: package sage-9.1-py37hc8dfbb8_0 requires python >=3.7,<3.8.0a0, but none of the providers can be installed

Pin flask-babel to 0.9

As sage notebook is incompatible with 0.11

Installation recommendation to use Python 3.9 not working with mambaforge

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

python 3.9 and 3.8 doesn't come with libgap.... so I am getting an error even though on the official sage documentation they provide 3.9 as an example version of python. Am I missing something? mamba create -n big-macs-llm sage python=3.9 installs sage without errors and I can import a number of things but when I try to import StandardTableaux I get an import name error referencing the libgap library.

Any recommendations?

conda install libgap
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - libgap

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Installed packages

# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
arb                       2.23.0               he5401aa_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38hb991d35_3    conda-forge
arpack                    3.7.0                h58ebc17_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
backports.zoneinfo        0.2.1            py38hb991d35_7    conda-forge
bdw-gc                    8.0.6                hc021e02_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
beniget                   0.4.1              pyhd8ed1ab_0    conda-forge
blas-devel                3.9.0           16_osxarm64_openblas    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
brial                     1.2.12             pyha3edaa6_0    conda-forge
brotli                    1.0.9                h1a8c8d9_8    conda-forge
brotli-bin                1.0.9                h1a8c8d9_8    conda-forge
brotlipy                  0.7.0           py38hb991d35_1005    conda-forge
bwidget                   1.9.14               hce30654_1    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.18.1               h3422bc3_0    conda-forge
ca-certificates           2022.12.7            h4653dfc_0    conda-forge
cairo                     1.16.0            h73a0509_1014    conda-forge
cctools_osx-arm64         973.0.1             hef52d2f_13    conda-forge
cddlib                    1!0.94m              h6d7a090_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py38ha45ccd6_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
clang                     14.0.6               hce30654_0    conda-forge
clang-14                  14.0.6          default_h81a5282_0    conda-forge
clang_osx-arm64           14.0.6               h15773ab_6    conda-forge
clangxx                   14.0.6          default_hb7ecf47_0    conda-forge
clangxx_osx-arm64         14.0.6               he29aa18_6    conda-forge
cliquer                   1.22                 h27ca646_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
compiler-rt               14.0.6               h30b49de_0    conda-forge
compiler-rt_osx-arm64     14.0.6               h48302dc_0    conda-forge
contourpy                 1.0.7            py38h9dc3d6a_0    conda-forge
cryptography              40.0.1           py38h23f6d3d_0    conda-forge
curl                      7.88.1               h9049daf_1    conda-forge
cvxopt                    1.3.0            py38hd15c5c0_4    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cypari2                   2.1.3            py38h18f8f8f_1    conda-forge
cysignals                 1.11.2           py38h57b977d_1    conda-forge
cython                    0.29.34          py38h2b1e499_0    conda-forge
debugpy                   1.6.7            py38h2b1e499_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.19             py38h10201cd_1    conda-forge
dsdp                      5.8               h9397a75_1203    conda-forge
ecl                       21.2.1               h8492d4d_2    conda-forge
eclib                     20221012             h099c6ef_1    conda-forge
ecm                       7.0.4             h47c7c1a_1002    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hb7217d7_1    conda-forge
fflas-ffpack              2.4.3                h11f2abc_2    conda-forge
fftw                      3.3.10          nompi_h3046061_107    conda-forge
flintqs                   1.0               ha2e105b_1001    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.3           py38hb991d35_0    conda-forge
fplll                     5.4.4                h29209e0_0    conda-forge
fpylll                    0.5.9            py38hfed99dd_0    conda-forge
freetype                  2.12.1               hd633e50_1    conda-forge
fribidi                   1.0.10               h27ca646_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gap-core                  4.11.1               he8f4e70_5    conda-forge
gap-defaults              4.11.1               hce30654_5    conda-forge
gast                      0.5.3              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h0186832_0    conda-forge
gf2x                      1.3.0                hdaa854c_2    conda-forge
gfan                      0.6.2             hec08f5c_1003    conda-forge
gfortran_impl_osx-arm64   11.3.0              h2a9d086_31    conda-forge
gfortran_osx-arm64        11.3.0               h57527a5_1    conda-forge
giac                      1.9.0.21             h1c96721_1    conda-forge
giflib                    5.2.1                h1a8c8d9_3    conda-forge
givaro                    4.1.1                h76d1151_2    conda-forge
glpk                      5.0                  h6d7a090_0    conda-forge
gmp                       6.2.1                h9f76cd9_0    conda-forge
gmpy2                     2.1.2            py38h904d018_1    conda-forge
graphite2                 1.3.13            h9f76cd9_1001    conda-forge
gsl                       2.7                  h6e638da_0    conda-forge
harfbuzz                  6.0.0                hddbc195_0    conda-forge
icu                       70.1                 h6b3803e_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
igraph                    0.9.10               hcec9b84_1    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
iml                       1.0.5             hd52f0d1_1003    conda-forge
importlib-metadata        6.2.0              pyha770c72_0    conda-forge
importlib-resources       5.12.0             pyhd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.22.0             pyh736e0ef_0    conda-forge
ipython                   8.12.0             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.6              pyhd8ed1ab_0    conda-forge
isl                       0.25                 h9a09cb3_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jmol                      14.32.10             hce30654_0    conda-forge
jpeg                      9e                   h1a8c8d9_3    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_core              4.12.0           py38h10201cd_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.5.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.7              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.4            py38h9dc3d6a_1    conda-forge
krb5                      1.20.1               h69eda48_0    conda-forge
lcalc                     2.0.5                hc94e8e6_1    conda-forge
lcms2                     2.15                 h481adae_0    conda-forge
ld64_osx-arm64            609                 h7167370_13    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libbraiding               1.1                  h9f76cd9_0    conda-forge
libbrial                  1.2.12               he94e455_0    conda-forge
libbrotlicommon           1.0.9                h1a8c8d9_8    conda-forge
libbrotlidec              1.0.9                h1a8c8d9_8    conda-forge
libbrotlienc              1.0.9                h1a8c8d9_8    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libclang-cpp14            14.0.6          default_h81a5282_0    conda-forge
libcurl                   7.88.1               h9049daf_1    conda-forge
libcxx                    16.0.1               h75e25f2_0    conda-forge
libdeflate                1.17                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libexpat                  2.5.0                hb7217d7_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libflint                  2.9.0           h173eafc_ntl_100    conda-forge
libgd                     2.3.3                h90fb8ed_4    conda-forge
libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
libgfortran-devel_osx-arm64 11.3.0              hfe9555d_31    conda-forge
libgfortran5              12.2.0              h0eea778_31    conda-forge
libglib                   2.74.1               h4646484_1    conda-forge
libhomfly                 1.02r6               h27ca646_0    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
liblapacke                3.9.0           16_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hf6e71e7_1    conda-forge
libnghttp2                1.52.0               hae82a92_0    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.40.0               h76d750c_0    conda-forge
libssh2                   1.10.0               h7a5bd25_3    conda-forge
libtiff                   4.5.0                h5dffbdd_2    conda-forge
libwebp                   1.2.4                h999c80f_1    conda-forge
libwebp-base              1.2.4                h1a8c8d9_0    conda-forge
libxcb                    1.13              h9b22ae9_1004    conda-forge
libxml2                   2.10.3               h67585b2_4    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
linbox                    1.6.3                h549c411_7    conda-forge
llvm-openmp               16.0.1               h7cfbb63_0    conda-forge
llvm-tools                14.0.6               hf6e71e7_1    conda-forge
lrcalc                    2.1                  hb7217d7_4    conda-forge
m4ri                      20140914          h17b34a0_1005    conda-forge
m4rie                     20150908          h17b34a0_1001    conda-forge
make                      4.3                  he57ea6c_1    conda-forge
markupsafe                2.1.2            py38hb991d35_0    conda-forge
matplotlib-base           3.7.1            py38hbbe890c_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
maxima                    5.45.0               h6032a66_2    conda-forge
memory-allocator          0.1.2            py38hb991d35_2    conda-forge
metis                     5.1.0             h9f76cd9_1006    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                h91ba8db_0    conda-forge
mpfi                      1.5.4             hbde5f5b_1001    conda-forge
mpfr                      4.2.0                he09a6ba_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nauty                     2.7.2                h3422bc3_0    conda-forge
nbclassic                 0.5.5              pyhb4ecaf3_1    conda-forge
nbclient                  0.7.3              pyhd8ed1ab_0    conda-forge
nbconvert                 7.3.0              pyhd8ed1ab_2    conda-forge
nbconvert-core            7.3.0              pyhd8ed1ab_2    conda-forge
nbconvert-pandoc          7.3.0              pyhd8ed1ab_2    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  2.8.8              pyhd8ed1ab_0    conda-forge
notebook                  6.5.4              pyha770c72_0    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
ntl                       11.4.3               hbb3f309_1    conda-forge
numpy                     1.24.2           py38hac8ee1c_0    conda-forge
openblas                  0.3.21          openmp_hf78f355_3    conda-forge
openjdk                   17.0.3               hf913c23_6    conda-forge
openjpeg                  2.5.0                hbc2ba62_2    conda-forge
openssl                   3.1.0                h03a7124_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
palp                      2.20                 h27ca646_0    conda-forge
pandoc                    2.19.2               hce30654_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.14              h6c112b8_0    conda-forge
pari                      2.15.3          hee76a8e_2_pthread    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hb34f9b4_0    conda-forge
perl                      5.32.1          2_h9b22ae9_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0            py38h1bb68ce_1    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h27ca646_0    conda-forge
pkg-config                0.29.2            hab62308_1008    conda-forge
pkgconfig                 1.5.5              pyhd8ed1ab_4    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
planarity                 3.0.0.5           h27ca646_1002    conda-forge
platformdirs              3.2.0              pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
ppl                       1.2               h8b147cf_1006    conda-forge
pplpy                     0.8.6            py38h544d4bf_1    conda-forge
primecount                7.4                  h2e04ded_1    conda-forge
primecountpy              0.1.0            py38h7b951d2_2    conda-forge
primesieve                8.0                  h9a09cb3_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.4            py38hb991d35_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3           py38hb991d35_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.8.16          h3ba56d0_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-lrcalc             2.1              py38h2b1e499_4    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.8                      3_cp38    conda-forge
pythran                   0.12.1           py38he0a633c_0    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pytz-deprecation-shim     0.1.0.post0      py38h10201cd_3    conda-forge
pyyaml                    6.0              py38hb991d35_5    conda-forge
pyzmq                     24.0.1           py38hb72be9f_1    conda-forge
qd                        2.3.22            hbec66e7_1004    conda-forge
r-base                    4.2.3                heabe65b_0    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
requests                  2.28.2             pyhd8ed1ab_1    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpy2                      3.5.10          py38r42hb39dbe9_0    conda-forge
rubiks                    20070912          h9f76cd9_1001    conda-forge
rw                        0.9                  h3422bc3_0    conda-forge
sage                      9.8                  hd8ed1ab_0    conda-forge
sage-docbuild             9.8                      pypi_0    pypi
sage-setup                9.8                      pypi_0    pypi
sagelib                   9.8              py38h494b33e_2    conda-forge
sagemath-db-combinatorial-designs 20140630                      1    conda-forge
sagemath-db-conway-polynomials 0.5.0                h4653dfc_1    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20210214             hd8ed1ab_0    conda-forge
sagemath-db-polytopes     20170220                      1    conda-forge
sagemath-standard         9.8                      pypi_0    pypi
sagetex                   3.6.1              pyhd8ed1ab_0    conda-forge
scipy                     1.10.1           py38h7b4f323_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                67.6.1             pyhd8ed1ab_0    conda-forge
sigtool                   0.1.3                h44b9a77_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singular                  4.2.1.p3             hb77faed_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sphinx                    5.3.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlite                    3.40.0               h2229b38_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
suitesparse               5.10.1               h7cd81ec_1    conda-forge
symmetrica                3.0.1                hb7217d7_0    conda-forge
sympow                    2.023.6              hb0babe8_3    conda-forge
sympy                     1.11.1          pypyh9d50eac_103    conda-forge
tachyon                   0.99b6            hfb72b2a_1001    conda-forge
tapi                      1100.0.11            he4954df_0    conda-forge
tbb                       2021.8.0             hffc8910_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
three.js                  122                  hd8ed1ab_2    conda-forge
threejs-sage              122                  hd8ed1ab_2    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tktable                   2.10                 h4161312_3    conda-forge
tornado                   6.2              py38hb991d35_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
tzlocal                   4.3              py38h10201cd_0    conda-forge
unicodedata2              15.0.0           py38hb991d35_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.7              pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.9                h27ca646_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xsimd                     8.0.5                hc021e02_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zeromq                    4.3.4                hbdafb3b_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h03a7124_4    conda-forge
zn_poly                   0.9.2                h391046e_0    conda-forge
zstd                      1.5.2                hf913c23_6    conda-forge

Environment info

conda version : 23.1.0
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=arm64
                          __osx=12.6=0
                          __unix=0=0

Documentation access with ? or ?? not available

Issue: in the Sage console one should be able to access the documentation with a single question mark ? and the source code with two ??. However the following gives an error

sage: a = 1
sage: a?
ApplicationError                          Traceback (most recent call last)
<ipython-input-8-1cb05c887abe> in <module>()
----> 1 get_ipython().magic('pinfo2 a')
/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/interactiveshell.py in magic(self, arg_s)
   2158         magic_name, _, magic_arg_s = arg_s.partition(' ')
   2159         magic_name = magic_name.lstrip(prefilter.ESC_MAGIC)
-> 2160         return self.run_line_magic(magic_name, magic_arg_s)
   2161 
   2162     #-------------------------------------------------------------------------

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/interactiveshell.py in run_line_magic(self, magic_name, line)
   2079                 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
   2080             with self.builtin_trap:
-> 2081                 result = fn(*args,**kwargs)
   2082             return result
   2083 

</home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/decorator.py:decorator-gen-75> in pinfo2(self, parameter_s, namespaces)

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    186     # but it's overkill for just that one bit of state.
    187     def magic_deco(arg):
--> 188         call = lambda f, *a, **k: f(*a, **k)
    189 
    190         if callable(arg):

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/magics/namespace.py in pinfo2(self, parameter_s, namespaces)
     67         '%pinfo2 object' is just a synonym for object?? or ??object."""
     68         self.shell._inspect('pinfo', parameter_s, detail_level=1,
---> 69                             namespaces=namespaces)
     70 
     71     @skip_doctest

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/interactiveshell.py in _inspect(self, meth, oname, namespaces, **kw)
   1534             elif meth == 'pinfo':
   1535                 pmethod(info.obj, oname, formatter, info, 
-> 1536                         enable_html_pager=self.enable_html_pager, **kw)
   1537             else:
   1538                 pmethod(info.obj, oname)

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/oinspect.py in pinfo(self, obj, oname, formatter, info, detail_level, enable_html_pager)
    713         - detail_level: if set to 1, more information is given.
    714         """
--> 715         info = self._get_info(obj, oname, formatter, info, detail_level)
    716         if not enable_html_pager:
    717             del info['text/html']

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/oinspect.py in _get_info(self, obj, oname, formatter, info, detail_level)
    614         """Retrieve an info dict and format it."""
    615 
--> 616         info = self._info(obj, oname=oname, info=info, detail_level=detail_level)
    617 
    618         _mime = {
/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/IPython/core/oinspect.py in _info(self, obj, oname, info, detail_level)
    763                     ds += "\nDocstring:\n" + obj.__doc__
    764         else:
--> 765             ds = getdoc(obj)
    766             if ds is None:
    767                 ds = '<no docstring>'

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/sage/misc/lazy_import.pyx in sage.misc.lazy_import.LazyImport.__call__ (build/cythonized/sage/misc/lazy_import.c:3696)()
    352             True
    353         """
--> 354         return self.get_object()(*args, **kwds)
    355 
    356     def __repr__(self):

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/sage/misc/sageinspect.py in sage_getdoc(obj, obj_name, embedded_override)
   1930         return ''
   1931     r = sage_getdoc_original(obj)
-> 1932     s = sage.misc.sagedoc.format(r, embedded=(embedded_override or EMBEDDED_MODE))
   1933 
   1934     # Fix object naming

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/sage/misc/sagedoc.py in format(s, embedded)
    709             s = process_mathtt(s)
    710         s = process_extlinks(s, embedded=embedded)
--> 711         s = detex(s, embedded=embedded)
    712     return s
    713 

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/sage/misc/sagedoc.py in detex(s, embedded)
    226         s = _rmcmd(s, 'mathop')
    227         s = _rmcmd(s, 'mathrm')
--> 228         s = sphinxify(s, format='text')
    229         # Do math substitutions. The strings to be replaced should be
    230         # TeX commands like "\\blah". Do a regular expression

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/sage/misc/sphinxify.py in sphinxify(docstring, format)
     97     # buildername, confoverrides, status, warning, freshenv).
     98     sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format,
---> 99                         confoverrides, None, None, True)
    100     sphinx_app.build(None, [rst_name])
    101     sys.path = old_sys_path

/home/vincent/miniconda3/envs/sage/lib/python3.6/site-packages/sphinx/application.py in __init__(self, srcdir, confdir, outdir, doctreedir, buildername, confoverrides, status, warning, freshenv, warningiserror, tags, verbosity, parallel, keep_going)
    151             if not path.isfile(path.join(self.confdir, 'conf.py')):
    152                 raise ApplicationError(__("config directory doesn't contain a "
--> 153                                           "conf.py file (%s)") % confdir)
    154 
    155         if not path.isdir(self.srcdir):

ApplicationError: config directory doesn't contain a conf.py file (/home/vincent/miniconda3/envs/sage/src/doc/en/introspect)

Environment (conda list):

$ conda list
# packages in environment at /home/vincent/miniconda3/envs/sage:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1  
alabaster                 0.7.12                     py_0    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
arb                       2.16.0            hb20f59a_1000    conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
attrs                     19.1.0                     py_0    conda-forge
automat                   0.7.0                      py_1    conda-forge
babel                     2.7.0                      py_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.os              0.1.1                 py36_1001    conda-forge
bdw-gc                    8.0.4                h6bb024c_0    conda-forge
binutils_impl_linux-64    2.31.1               h6176602_1  
binutils_linux-64         2.31.1               h6176602_7  
bleach                    3.1.0                      py_0    conda-forge
boost-cpp                 1.69.0            h11c811c_1000    conda-forge
brial                     1.2.4                      py_1    conda-forge
bwidget                   1.9.11                        1  
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
cairo                     1.16.0            h18b612c_1001    conda-forge
cddlib                    1!0.94j           ha14ba45_1001    conda-forge
certifi                   2019.6.16                py36_0    conda-forge
cffi                      1.12.3           py36h8022711_0    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                        py_0    conda-forge
cliquer                   1.21                          0    conda-forge
constantly                15.1.0                     py_0    conda-forge
cryptography              2.7              py36h72c5cf5_0    conda-forge
curl                      7.64.1               hf8cf82a_0    conda-forge
cvxopt                    1.2.3           py36h915cfec_202    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cypari2                   2.1.1            py36hef3d0d6_0    conda-forge
cysignals                 1.10.2           py36he8bbba0_1    conda-forge
cython                    0.29.10          py36he1b5a44_0    conda-forge
dbus                      1.13.6               he372182_0    conda-forge
decorator                 4.4.0                      py_0    conda-forge
defusedxml                0.5.0                      py_1    conda-forge
docutils                  0.14                  py36_1001    conda-forge
dsdp                      5.8               h23d7751_1203    conda-forge
ecl                       16.1.2            h63faa73_1003    conda-forge
eclib                     20190226             h961da46_2    conda-forge
ecm                       7.0.4             ha14ba45_1002    conda-forge
entrypoints               0.3                   py36_1000    conda-forge
expat                     2.2.5             he1b5a44_1003    conda-forge
fastcache                 1.1.0            py36h516909a_0    conda-forge
fflas-ffpack              2.4.2                h042891f_1    conda-forge
fftw                      3.3.8           nompi_h7f3a6c3_1105    conda-forge
flask                     0.11.1                     py_1    conda-forge
flask-autoindex           0.6.2                      py_0    conda-forge
flask-babel               0.9                        py_0    conda-forge
flask-oldsessions         0.10                       py_0    conda-forge
flask-openid              1.2.5                 py36_1003    conda-forge
flask-silk                0.2                        py_0    conda-forge
flintqs                   1.0                           0    conda-forge
fontconfig                2.13.1            he4413a7_1000    conda-forge
fplll                     5.2.1             h4d64954_1000    conda-forge
fpylll                    0.4.1dev        py36h940fe96_1000    conda-forge
freetype                  2.10.0               he983fc9_0    conda-forge
future                    0.17.1                py36_1000    conda-forge
gap                       4.10.1               hee7d332_4    conda-forge
gap-core                  4.10.1               h711559f_4    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_7    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
gf2x                      1.2               ha03fbb7_1003    conda-forge
gfan                      0.6.2                h0eace8b_1    conda-forge
gfortran_impl_linux-64    7.3.0                hdf63c60_1  
gfortran_linux-64         7.3.0                h553295d_7  
giac                      1.5.0.37             h8b4616e_1    conda-forge
giflib                    5.1.9                h516909a_0    conda-forge
givaro                    4.1.1                h192cbe9_0    conda-forge
glib                      2.58.3            h6f030ca_1001    conda-forge
glpk                      4.65              ha14ba45_1001    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gmpy2                     2.1.0b1          py36h04dde30_0    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.5                  h294904e_0    conda-forge
gst-plugins-base          1.14.5               h0935bb2_0    conda-forge
gstreamer                 1.14.5               h36ae1b5_0    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_7    conda-forge
harfbuzz                  2.4.0                h37c48d4_1    conda-forge
hyperlink                 17.3.1                     py_0    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                   py36_1000    conda-forge
imagesize                 1.1.0                      py_0    conda-forge
iml                       1.0.5             h3057dec_1002    conda-forge
importlib_metadata        0.18                     py36_0    conda-forge
incremental               17.5.0                     py_0    conda-forge
ipykernel                 4.10.0                   py36_1    conda-forge
ipython                   5.8.0                    py36_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
itsdangerous              1.1.0                      py_0    conda-forge
jinja2                    2.10.1                     py_0    conda-forge
jmol                      14.29.15                      1    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.0.0a3               py36_1000    conda-forge
jupyter_client            5.2.4                      py_3    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
kiwisolver                1.1.0            py36hc9558a2_0    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
lcalc                     1.23              hab5a3d0_1002    conda-forge
libblas                   3.8.0                7_openblas    conda-forge
libbraiding               1.0                  he1b5a44_0    conda-forge
libbrial                  1.2.4                hcdf1f5c_0    conda-forge
libcblas                  3.8.0                7_openblas    conda-forge
libcurl                   7.64.1               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libflint                  2.5.2             h3fb3072_1003    conda-forge
libgcc-ng                 9.1.0                hdf63c60_0  
libgd                     2.2.5             h0d07dcb_1005    conda-forge
libgfortran-ng            7.3.0                hdf63c60_0  
libhomfly                 1.02r6               h516909a_0    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0                7_openblas    conda-forge
liblapacke                3.8.0                7_openblas    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libsemigroups             0.6.7                he1b5a44_0    conda-forge
libsodium                 1.0.16            h14c3975_1001    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.1.0                hdf63c60_0  
libtiff                   4.0.10            h57b8799_1003    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp                   1.0.2                h576950b_1    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.9                h13577e0_0    conda-forge
linbox                    1.6.3                h03cd913_2    conda-forge
lrcalc                    1.2               hf484d3e_1000    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
m4ri                      20140914          he983fc9_1004    conda-forge
m4rie                     20150908          h3cfcefd_1000    conda-forge
make                      4.2.1             h14c3975_2004    conda-forge
markupsafe                1.1.1            py36h14c3975_0    conda-forge
matplotlib                2.2.3            py36hb69df0a_0  
maxima                    5.42.2               h63faa73_1    conda-forge
metis                     5.1.0             hf484d3e_1003    conda-forge
mistune                   0.8.4           py36h14c3975_1000    conda-forge
mpc                       1.1.0             hb20f59a_1006    conda-forge
mpfi                      1.5.4             hb20f59a_1001    conda-forge
mpfr                      4.0.2                ha14ba45_0    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
nauty                     2.6.7             h14c3975_1000    conda-forge
nbconvert                 5.5.0                      py_0    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
networkx                  2.3                        py_0    conda-forge
normaliz                  3.7.3                h8b68381_1    conda-forge
notebook                  5.7.8                    py36_1    conda-forge
ntl                       11.3.2            h52520da_1000    conda-forge
numpy                     1.16.4           py36h95a1406_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.3.5             h9ac9557_1001    conda-forge
openjdk                   11.0.1            h516909a_1016    conda-forge
openssl                   1.1.1b               h14c3975_1    conda-forge
packaging                 19.0                       py_0    conda-forge
palp                      2.1                           0    conda-forge
pandoc                    2.7.3                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.40.14           h4ea9474_1004    conda-forge
pari                      2.11.1          pl526h7ba8bfb_0    conda-forge
path.py                   12.0.1                     py_0    conda-forge
pathlib2                  2.3.3                 py36_1000    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
perl                      5.26.2            h516909a_1006    conda-forge
pexpect                   4.7.0                    py36_0    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pillow                    5.4.1           py36h00a061d_1000    conda-forge
pip                       19.1.1                   py36_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
pkgconfig                 1.3.1                 py36_1001    conda-forge
planarity                 3.0.0.5           h14c3975_1002    conda-forge
ppl                       1.2               h64e95d0_1002    conda-forge
pplpy                     0.8.4            py36h9603a25_0    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt_toolkit            1.0.15                     py_1    conda-forge
psutil                    5.6.3            py36h516909a_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pyasn1                    0.4.5                      py_0    conda-forge
pyasn1-modules            0.2.5                      py_0    conda-forge
pycparser                 2.19                     py36_1    conda-forge
pygments                  2.4.2                      py_0    conda-forge
pyhamcrest                1.9.0                      py_2    conda-forge
pynac                     0.7.25           py36h58d1e65_3    conda-forge
pyopenssl                 19.0.0                   py36_0    conda-forge
pyparsing                 2.4.0                      py_0    conda-forge
pyqt                      5.9.2            py36hcca6a23_0    conda-forge
pyrsistent                0.15.2           py36h516909a_0    conda-forge
pysocks                   1.7.0                    py36_0    conda-forge
python                    3.6.7             h381d211_1004    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
python3-openid            3.1.0                 py36_1001    conda-forge
pytz                      2019.1                     py_0    conda-forge
pyzmq                     17.1.2           py36he6710b0_2  
qd                        2.3.22            h1c2f66e_1002    conda-forge
qt                        5.9.7                h52cfd70_2    conda-forge
r-assertthat              0.2.1            r351h6115d3f_0    conda-forge
r-backports               1.1.4            r351hcdcec82_0    conda-forge
r-base                    3.5.1             hea2b9be_1007    conda-forge
r-bh                      1.69.0_1         r351h6115d3f_0    conda-forge
r-bit                     1.1_14           r351hcdcec82_0    conda-forge
r-bit64                   0.9_7           r351h96ca727_1000    conda-forge
r-blob                    1.1.1                 r351_1001    conda-forge
r-cli                     1.1.0            r351h6115d3f_0    conda-forge
r-crayon                  1.3.4           r351h6115d3f_1001    conda-forge
r-dbi                     1.0.0           r351h6115d3f_1001    conda-forge
r-dbplyr                  1.4.2             r35h6115d3f_0    conda-forge
r-digest                  0.6.19           r351h0357c0b_0    conda-forge
r-dplyr                   0.8.1            r351h0357c0b_0    conda-forge
r-fansi                   0.4.0           r351h96ca727_1000    conda-forge
r-glue                    1.3.1            r351hcdcec82_0    conda-forge
r-magrittr                1.5             r351h6115d3f_1001    conda-forge
r-memoise                 1.1.0           r351h6115d3f_1001    conda-forge
r-pillar                  1.4.1                h6115d3f_0    conda-forge
r-pkgconfig               2.0.2           r351h6115d3f_1001    conda-forge
r-plogr                   0.2.0           r351h6115d3f_1001    conda-forge
r-prettyunits             1.0.2           r351h6115d3f_1001    conda-forge
r-purrr                   0.3.2            r351hcdcec82_0    conda-forge
r-r6                      2.4.0            r351h6115d3f_0    conda-forge
r-rcpp                    1.0.1            r351h0357c0b_0    conda-forge
r-rlang                   0.3.4            r351hcdcec82_0    conda-forge
r-rsqlite                 2.1.1           r351h29659fb_1000    conda-forge
r-tibble                  2.1.3             r35hcdcec82_0    conda-forge
r-tidyselect              0.2.5           r351h29659fb_1000    conda-forge
r-utf8                    1.1.4           r351h96ca727_1000    conda-forge
r-vctrs                   0.1.0           r351h96ca727_1000    conda-forge
r-zeallot                 0.1.0           r351h6115d3f_1000    conda-forge
ratpoints                 2.1.3             ha14ba45_1002    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
requests                  2.22.0                   py36_0    conda-forge
rpy2                      2.9.4           py36r351h941a26a_1    conda-forge
rubiks                    20070912          hf484d3e_1001    conda-forge
rw                        0.7                           1    conda-forge
sage                      8.8.rc1          py36hcb32578_0    conda-forge
sagelib                   8.8.rc1          py36h21c7cb8_1    conda-forge
sagemath-db-combinatorial-designs 20140630                      1    conda-forge
sagemath-db-conway-polynomials 0.5.0            py36hecc5488_0    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20161026                      1    conda-forge
sagemath-db-polytopes     20170220                      1    conda-forge
sagenb                    1.1.2                      py_0    conda-forge
scipy                     1.3.0            py36h921218d_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
service_identity          18.1.0                     py_0    conda-forge
setuptools                41.0.1                   py36_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singledispatch            3.4.0.3               py36_1000    conda-forge
singular                  4.1.2.p1             hdd094a0_2    conda-forge
sip                       4.19.8          py36hf484d3e_1000    conda-forge
six                       1.12.0                py36_1000    conda-forge
snowballstemmer           1.2.1                      py_1    conda-forge
speaklater                1.3                        py_3    conda-forge
sphinx                    1.8.5                    py36_0    conda-forge
sphinxcontrib-websupport  1.1.2                      py_0    conda-forge
sqlite                    3.28.0               h8b20d00_0    conda-forge
suitesparse               4.5.6             heab0a99_1202    conda-forge
symmetrica                2.0                           0    conda-forge
sympow                    1.018.1                       1    conda-forge
sympy                     1.4                      py36_0    conda-forge
tachyon                   0.99b6                        0    conda-forge
tbb                       2019.7               hc9558a2_0    conda-forge
terminado                 0.8.2                    py36_0    conda-forge
testpath                  0.4.2                   py_1001    conda-forge
tk                        8.6.9             hed695b0_1002    conda-forge
tktable                   2.10                 h14c3975_0  
tornado                   4.5.3           py36h14c3975_1001    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
twisted                   18.9.0          py36h14c3975_1000    conda-forge
tzlocal                   1.5.1                      py_0    conda-forge
urllib3                   1.24.3                   py36_0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  0.15.4                     py_0    conda-forge
wheel                     0.33.4                   py36_0    conda-forge
widgetsnbextension        3.4.2                 py36_1000    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h516909a_1004    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            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                        5.2.4             h14c3975_1001    conda-forge
zeromq                    4.3.1             hf484d3e_1000    conda-forge
zipp                      0.5.1                      py_0    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge
zn_poly                   0.9.1                he80fd80_0    conda-forge
zope.interface            4.6.0           py36h14c3975_1000    conda-forge
zstd                      1.4.0                h3b9ef0a_0    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : sage
    active env location : /home/vincent/miniconda3/envs/sage
            shell level : 1
       user config file : /home/vincent/.condarc
 populated config files : /home/vincent/.condarc
          conda version : 4.6.14
    conda-build version : not installed
         python version : 3.7.3.final.0
       base environment : /home/vincent/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/vincent/miniconda3/pkgs
                          /home/vincent/.conda/pkgs
       envs directories : /home/vincent/miniconda3/envs
                          /home/vincent/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.14 requests/2.22.0 CPython/3.7.3 Linux/5.1.6-arch1-1-ARCH arch/rolling glibc/2.29
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

sage cli not working

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

I have a setup as described in #86, basically:

M1 Mac, installed the following:

• homebrew
• pyenv
• anaconda 2023-03
• deleted ~/.condarc file
• followed instructions creating virtual environment with sage as described here

I have activated my virtual environment, and can run what I want to run using Jupyter notebook. It works well. However, when I am on the command line, I cannot run sage successfully. This is not critical path for me, so prioritize this ticket as you wish, I did want to show you my output:

$ (myenv) sage
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-config: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-config: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-venv-config: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-ipython: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: line 310: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-ipython: Undefined error: 0
(big-macs-llm) (anaconda3-2023.03) ➜  big-macs-llm-old git:(main) ✗ sage
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-config: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-config: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-venv-config: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-ipython: /Users/runner/miniforge3/conda-bld/sagelib_1676643843996/_build_env/venv/bin/c: bad interpreter: No such file or directory
/Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage: line 310: /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/big-macs-llm/bin/sage-ipython: Undefined error: 0

Installed packages

# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
arb                       2.23.0               he5401aa_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h8e9501a_3    conda-forge
arpack                    3.7.0                h58ebc17_2    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bdw-gc                    8.0.6                hc021e02_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
beniget                   0.4.1              pyhd8ed1ab_0    conda-forge
blas-devel                3.9.0           16_osxarm64_openblas    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
brial                     1.2.12             pyha3edaa6_0    conda-forge
brotli                    1.0.9                h1a8c8d9_8    conda-forge
brotli-bin                1.0.9                h1a8c8d9_8    conda-forge
brotlipy                  0.7.0           py310h8e9501a_1005    conda-forge
bwidget                   1.9.14               hce30654_1    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.18.1               h3422bc3_0    conda-forge
ca-certificates           2022.12.7            h4653dfc_0    conda-forge
cairo                     1.16.0            h73a0509_1014    conda-forge
cctools_osx-arm64         973.0.1             hef52d2f_13    conda-forge
cddlib                    1!0.94m              h6d7a090_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h2399d43_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
clang                     14.0.6               hce30654_0    conda-forge
clang-14                  14.0.6          default_h81a5282_0    conda-forge
clang_osx-arm64           14.0.6               h15773ab_6    conda-forge
clangxx                   14.0.6          default_hb7ecf47_0    conda-forge
clangxx_osx-arm64         14.0.6               he29aa18_6    conda-forge
cliquer                   1.22                 h27ca646_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
compiler-rt               14.0.6               h30b49de_0    conda-forge
compiler-rt_osx-arm64     14.0.6               h48302dc_0    conda-forge
contourpy                 1.0.7           py310h2887b22_0    conda-forge
cryptography              40.0.1          py310hfc83b78_0    conda-forge
curl                      7.88.1               h9049daf_1    conda-forge
cvxopt                    1.3.0           py310h3e41943_4    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cypari2                   2.1.3           py310hcb7f4b8_1    conda-forge
cysignals                 1.11.2          py310h1e2580b_1    conda-forge
cython                    0.29.34         py310h0f1eb42_0    conda-forge
debugpy                   1.6.7           py310h0f1eb42_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.19            py310hbe9552e_1    conda-forge
dsdp                      5.8               h9397a75_1203    conda-forge
ecl                       21.2.1               h8492d4d_2    conda-forge
eclib                     20221012             h099c6ef_1    conda-forge
ecm                       7.0.4             h47c7c1a_1002    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hb7217d7_1    conda-forge
fflas-ffpack              2.4.3                h11f2abc_2    conda-forge
fftw                      3.3.10          nompi_h3046061_107    conda-forge
flintqs                   1.0               ha2e105b_1001    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.39.3          py310h8e9501a_0    conda-forge
fplll                     5.4.4                h29209e0_0    conda-forge
fpylll                    0.5.9           py310h57936e3_0    conda-forge
freetype                  2.12.1               hd633e50_1    conda-forge
fribidi                   1.0.10               h27ca646_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gap-core                  4.11.1               he8f4e70_5    conda-forge
gap-defaults              4.11.1               hce30654_5    conda-forge
gast                      0.5.3              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h0186832_0    conda-forge
gf2x                      1.3.0                hdaa854c_2    conda-forge
gfan                      0.6.2             hec08f5c_1003    conda-forge
gfortran_impl_osx-arm64   11.3.0              h2a9d086_31    conda-forge
gfortran_osx-arm64        11.3.0               h57527a5_1    conda-forge
giac                      1.9.0.21             h1c96721_1    conda-forge
giflib                    5.2.1                h1a8c8d9_3    conda-forge
givaro                    4.1.1                h76d1151_2    conda-forge
glpk                      5.0                  h6d7a090_0    conda-forge
gmp                       6.2.1                h9f76cd9_0    conda-forge
gmpy2                     2.1.2           py310h2e6cad2_1    conda-forge
graphite2                 1.3.13            h9f76cd9_1001    conda-forge
gsl                       2.7                  h6e638da_0    conda-forge
harfbuzz                  6.0.0                hddbc195_0    conda-forge
icu                       70.1                 h6b3803e_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
igraph                    0.9.10               hcec9b84_1    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
iml                       1.0.5             hd52f0d1_1003    conda-forge
importlib-metadata        6.2.1              pyha770c72_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.22.0             pyh736e0ef_0    conda-forge
ipython                   8.12.0             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.6              pyhd8ed1ab_0    conda-forge
isl                       0.25                 h9a09cb3_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jmol                      14.32.10             hce30654_0    conda-forge
jpeg                      9e                   h1a8c8d9_3    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_core              4.12.0          py310hbe9552e_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.5.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.7              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.4           py310h2887b22_1    conda-forge
krb5                      1.20.1               h69eda48_0    conda-forge
lcalc                     2.0.5                hc94e8e6_1    conda-forge
lcms2                     2.15                 h481adae_0    conda-forge
ld64_osx-arm64            609                 h7167370_13    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libbraiding               1.1                  h9f76cd9_0    conda-forge
libbrial                  1.2.12               he94e455_0    conda-forge
libbrotlicommon           1.0.9                h1a8c8d9_8    conda-forge
libbrotlidec              1.0.9                h1a8c8d9_8    conda-forge
libbrotlienc              1.0.9                h1a8c8d9_8    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libclang-cpp14            14.0.6          default_h81a5282_0    conda-forge
libcurl                   7.88.1               h9049daf_1    conda-forge
libcxx                    16.0.1               h75e25f2_0    conda-forge
libdeflate                1.17                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libexpat                  2.5.0                hb7217d7_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libflint                  2.9.0           h173eafc_ntl_100    conda-forge
libgd                     2.3.3                h90fb8ed_4    conda-forge
libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
libgfortran-devel_osx-arm64 11.3.0              hfe9555d_31    conda-forge
libgfortran5              12.2.0              h0eea778_31    conda-forge
libglib                   2.74.1               h4646484_1    conda-forge
libhomfly                 1.02r6               h27ca646_0    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
liblapacke                3.9.0           16_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hf6e71e7_1    conda-forge
libnghttp2                1.52.0               hae82a92_0    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.40.0               h76d750c_0    conda-forge
libssh2                   1.10.0               h7a5bd25_3    conda-forge
libtiff                   4.5.0                h5dffbdd_2    conda-forge
libwebp                   1.2.4                h999c80f_1    conda-forge
libwebp-base              1.2.4                h1a8c8d9_0    conda-forge
libxcb                    1.13              h9b22ae9_1004    conda-forge
libxml2                   2.10.3               h67585b2_4    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
linbox                    1.6.3                h549c411_7    conda-forge
llvm-openmp               16.0.1               h7cfbb63_0    conda-forge
llvm-tools                14.0.6               hf6e71e7_1    conda-forge
lrcalc                    2.1                  hb7217d7_4    conda-forge
m4ri                      20140914          h17b34a0_1005    conda-forge
m4rie                     20150908          h17b34a0_1001    conda-forge
make                      4.3                  he57ea6c_1    conda-forge
markupsafe                2.1.2           py310h8e9501a_0    conda-forge
matplotlib-base           3.7.1           py310h78c5c2f_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
maxima                    5.45.0               h6032a66_2    conda-forge
memory-allocator          0.1.2           py310h8e9501a_2    conda-forge
metis                     5.1.0             h9f76cd9_1006    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                h91ba8db_0    conda-forge
mpfi                      1.5.4             hbde5f5b_1001    conda-forge
mpfr                      4.2.0                he09a6ba_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nauty                     2.7.2                h3422bc3_0    conda-forge
nbclassic                 0.5.5              pyhb4ecaf3_1    conda-forge
nbclient                  0.7.3              pyhd8ed1ab_0    conda-forge
nbconvert                 7.3.0              pyhd8ed1ab_2    conda-forge
nbconvert-core            7.3.0              pyhd8ed1ab_2    conda-forge
nbconvert-pandoc          7.3.0              pyhd8ed1ab_2    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  2.8.8              pyhd8ed1ab_0    conda-forge
notebook                  6.5.4              pyha770c72_0    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
ntl                       11.4.3               hbb3f309_1    conda-forge
numpy                     1.24.2          py310h3d2048e_0    conda-forge
openblas                  0.3.21          openmp_hf78f355_3    conda-forge
openjdk                   17.0.3               hf913c23_6    conda-forge
openjpeg                  2.5.0                hbc2ba62_2    conda-forge
openssl                   3.1.0                h03a7124_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
palp                      2.20                 h27ca646_0    conda-forge
pandoc                    2.19.2               hce30654_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.14              h6c112b8_0    conda-forge
pari                      2.15.3          hee76a8e_2_pthread    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hb34f9b4_0    conda-forge
perl                      5.32.1          2_h9b22ae9_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.4.0           py310h5a7539a_1    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h27ca646_0    conda-forge
pkg-config                0.29.2            hab62308_1008    conda-forge
pkgconfig                 1.5.5              pyhd8ed1ab_4    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
planarity                 3.0.0.5           h27ca646_1002    conda-forge
platformdirs              3.2.0              pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
ppl                       1.2               h8b147cf_1006    conda-forge
pplpy                     0.8.6           py310h295cbc6_1    conda-forge
primecount                7.4                  h2e04ded_1    conda-forge
primecountpy              0.1.0           py310hbdd6ae5_2    conda-forge
primesieve                8.0                  h9a09cb3_0    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.4           py310h8e9501a_0    conda-forge
pthread-stubs             0.4               h27ca646_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3          py310h8e9501a_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.10         h3ba56d0_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-lrcalc             2.1             py310h0f1eb42_4    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    3_cp310    conda-forge
pythran                   0.12.1          py310h629746b_0    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pytz-deprecation-shim     0.1.0.post0     py310hbe9552e_3    conda-forge
pyyaml                    6.0             py310h8e9501a_5    conda-forge
pyzmq                     24.0.1          py310hc407298_1    conda-forge
qd                        2.3.22            hbec66e7_1004    conda-forge
r-base                    4.2.3                heabe65b_0    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
requests                  2.28.2             pyhd8ed1ab_1    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpy2                      3.5.10          py310r42hf1a086a_0    conda-forge
rubiks                    20070912          h9f76cd9_1001    conda-forge
rw                        0.9                  h3422bc3_0    conda-forge
sage                      9.8                  hd8ed1ab_0    conda-forge
sage-docbuild             9.8                      pypi_0    pypi
sage-setup                9.8                      pypi_0    pypi
sagelib                   9.8             py310h55faf8f_2    conda-forge
sagemath-db-combinatorial-designs 20140630                      1    conda-forge
sagemath-db-conway-polynomials 0.5.0                h4653dfc_1    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20210214             hd8ed1ab_0    conda-forge
sagemath-db-polytopes     20170220                      1    conda-forge
sagemath-standard         9.8                      pypi_0    pypi
sagetex                   3.6.1              pyhd8ed1ab_0    conda-forge
scipy                     1.10.1          py310ha0d8a01_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                67.6.1             pyhd8ed1ab_0    conda-forge
sigtool                   0.1.3                h44b9a77_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singular                  4.2.1.p3             hb77faed_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sphinx                    5.3.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlite                    3.40.0               h2229b38_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
suitesparse               5.10.1               h7cd81ec_1    conda-forge
symmetrica                3.0.1                hb7217d7_0    conda-forge
sympow                    2.023.6              hb0babe8_3    conda-forge
sympy                     1.11.1          pypyh9d50eac_103    conda-forge
tachyon                   0.99b6            hfb72b2a_1001    conda-forge
tapi                      1100.0.11            he4954df_0    conda-forge
tbb                       2021.8.0             hffc8910_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
three.js                  122                  hd8ed1ab_2    conda-forge
threejs-sage              122                  hd8ed1ab_2    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tktable                   2.10                 h4161312_3    conda-forge
tornado                   6.2             py310h8e9501a_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
tzlocal                   4.3             py310hbe9552e_0    conda-forge
unicodedata2              15.0.0          py310h8e9501a_0    conda-forge
urllib3                   1.26.15            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.7              pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.9                h27ca646_0    conda-forge
xorg-libxdmcp             1.1.3                h27ca646_0    conda-forge
xsimd                     8.0.5                hc021e02_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
zeromq                    4.3.4                hbdafb3b_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h03a7124_4    conda-forge
zn_poly                   0.9.2                h391046e_0    conda-forge
zstd                      1.5.2                hf913c23_6    conda-forge

Environment info

active environment : myenv
    active env location : /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/myenv
            shell level : 3
       user config file : /Users/steven/.condarc
 populated config files : /Users/steven/.condarc
          conda version : 23.3.1
    conda-build version : 3.24.0
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=arm64
                          __osx=12.6=0
                          __unix=0=0
       base environment : /Users/steven/.pyenv/versions/anaconda3-2023.03  (writable)
      conda av data dir : /Users/steven/.pyenv/versions/anaconda3-2023.03/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/steven/.pyenv/versions/anaconda3-2023.03/pkgs
                          /Users/steven/.conda/pkgs
       envs directories : /Users/steven/.pyenv/versions/anaconda3-2023.03/envs
                          /Users/steven/.conda/envs
               platform : osx-arm64
             user-agent : conda/23.3.1 requests/2.28.2 CPython/3.10.10 Darwin/21.6.0 OSX/12.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Package for aarch64 architecture is currently broken

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

I was building a CI container image for both x86_64 and aarch64 architectures installing sage from micromamba as suggested by the documentation, and I realized that the same image was not working for the ARM architecture.

[user@host]~% podman run -it --rm localhost/test_image /bin/bash
root@d65e0a177de4:/# source /root/.bashrc
root@d65e0a177de4:/# micromamba activate base
(base) root@d65e0a177de4:/# sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.7, Release Date: 2022-09-19                     │
│ Using Python 3.10.8. Type "help()" for help.                       │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: sage.all is not available; this is a limited REPL.        ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
Traceback (most recent call last):
  File "/root/micromamba/bin/sage-ipython", line 12, in <module>
    from sage.repl.interpreter import SageTerminalApp
  File "/root/micromamba/lib/python3.10/site-packages/sage/repl/interpreter.py", line 144, in <module>
    from sage.repl.preparse import preparse, containing_block
  File "/root/micromamba/lib/python3.10/site-packages/sage/repl/preparse.py", line 245, in <module>
    from sage.repl.load import load_wrap
  File "/root/micromamba/lib/python3.10/site-packages/sage/repl/load.py", line 16, in <module>
    from sage.cpython.string import str_to_bytes, bytes_to_str, FS_ENCODING
ModuleNotFoundError: No module named 'sage.cpython.string'

I paste here a minimal Dockerfile to reproduce the error, which can be generated with podman build . -t test_image:

FROM docker.io/debian:latest

USER root

RUN apt-get update \
    && DEBIAN_FRONTEND=noninteractive \
       apt-get install --no-install-recommends -y \
                        ca-certificates \
                        curl \
                        bzip2 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

RUN "${SHELL}" <(curl -L micro.mamba.pm/install.sh)

RUN bash -c "source /root/.bashrc ; micromamba install -y -n base -c conda-forge sage \
    && micromamba clean --all --yes"

I already tested:

• different base images (Ubuntu jammy, Fedora 37)
• directly using the micromamba docker image
• use the environment file with the same packages and versions of the x86_64 working image

By contrast, the sagemath package distributed through Debian repository is working fine.

Please note that:

• the error is present only on aarch64 ARM architecture (I am using an Oracle Ampere A1 instance)
• podman is a drop-in replacement to docker command (within this context)

Installed packages

List of packages in environment: "/root/micromamba"

  Name                               Version       Build                     Channel
──────────────────────────────────────────────────────────────────────────────────────────
  _ipython_minor_entry_point         8.7.0         hb6b4a82_0                conda-forge
  _openmp_mutex                      4.5           2_gnu                     conda-forge
  _r-mutex                           1.0.1         anacondar_1               conda-forge
  alabaster                          0.7.12        py_0                      conda-forge
  alsa-lib                           1.2.8         h4e544f5_0                conda-forge
  anyio                              3.6.2         pyhd8ed1ab_0              conda-forge
  arb                                2.23.0        h37d5dab_0                conda-forge
  argon2-cffi                        21.3.0        pyhd8ed1ab_0              conda-forge
  argon2-cffi-bindings               21.2.0        py310h761cc84_3           conda-forge
  arpack                             3.7.0         hf862f49_2                conda-forge
  asttokens                          2.2.1         pyhd8ed1ab_0              conda-forge
  attrs                              22.1.0        pyh71513ae_1              conda-forge
  babel                              2.11.0        pyhd8ed1ab_0              conda-forge
  backcall                           0.2.0         pyh9f0ad1d_0              conda-forge
  backports                          1.0           pyhd8ed1ab_3              conda-forge
  backports.functools_lru_cache      1.6.4         pyhd8ed1ab_0              conda-forge
  bdw-gc                             8.0.6         hd62202e_0                conda-forge
  beautifulsoup4                     4.11.1        pyha770c72_0              conda-forge
  beniget                            0.4.1         pyhd8ed1ab_0              conda-forge
  binutils_impl_linux-aarch64        2.39          h48546ad_1                conda-forge
  binutils_linux-aarch64             2.39          h489c705_11               conda-forge
  blas-devel                         3.9.0         16_linuxaarch64_openblas  conda-forge
  bleach                             4.1.0         pyhd8ed1ab_0              conda-forge
  brial                              1.2.11        pyh694c41f_0              conda-forge
  brotli                             1.0.9         h4e544f5_8                conda-forge
  brotli-bin                         1.0.9         h4e544f5_8                conda-forge
  brotlipy                           0.7.0         py310h761cc84_1005        conda-forge
  bwidget                            1.9.14        h8af1aa0_1                conda-forge
  bzip2                              1.0.8         hf897c2e_4                conda-forge
  c-ares                             1.18.1        hf897c2e_0                conda-forge
  ca-certificates                    2022.12.7     h4fd8a4c_0                conda-forge
  cairo                              1.16.0        hd19fb6e_1014             conda-forge
  cddlib                             1!0.94m       h719063d_0                conda-forge
  certifi                            2022.12.7     pyhd8ed1ab_0              conda-forge
  cffi                               1.15.1        py310hf0c4615_2           conda-forge
  charset-normalizer                 2.1.1         pyhd8ed1ab_0              conda-forge
  cliquer                            1.22          hb9de7d4_0                conda-forge
  colorama                           0.4.6         pyhd8ed1ab_0              conda-forge
  comm                               0.1.1         pyhd8ed1ab_0              conda-forge
  contourpy                          1.0.6         py310hb15e014_0           conda-forge
  cryptography                       38.0.4        py310h674ca28_0           conda-forge
  curl                               7.86.0        h22f3f83_1                conda-forge
  cvxopt                             1.3.0         py310haa23bb0_4           conda-forge
  cycler                             0.11.0        pyhd8ed1ab_0              conda-forge
  cypari2                            2.1.3         py310h0792cfb_0           conda-forge
  cysignals                          1.11.2        py310h87d4683_0           conda-forge
  cython                             0.29.32       py310h130cc07_1           conda-forge
  debugpy                            1.6.4         py310h130cc07_0           conda-forge
  decorator                          5.1.1         pyhd8ed1ab_0              conda-forge
  defusedxml                         0.7.1         pyhd8ed1ab_0              conda-forge
  docutils                           0.17.1        py310hbbe02a8_3           conda-forge
  dsdp                               5.8           hb12102e_1203             conda-forge
  ecl                                21.2.1        haa44c19_2                conda-forge
  eclib                              20220621      h87efab1_1                conda-forge
  ecm                                7.0.4         h719063d_1002             conda-forge
  entrypoints                        0.4           pyhd8ed1ab_0              conda-forge
  executing                          1.2.0         pyhd8ed1ab_0              conda-forge
  expat                              2.5.0         ha18d298_0                conda-forge
  fflas-ffpack                       2.4.3         hf104d39_2                conda-forge
  fftw                               3.3.10        nompi_ha1d0423_106        conda-forge
  flintqs                            1.0           h5fb5790_1001             conda-forge
  flit-core                          3.8.0         pyhd8ed1ab_0              conda-forge
  font-ttf-dejavu-sans-mono          2.37          hab24e00_0                conda-forge
  font-ttf-inconsolata               3.000         h77eed37_0                conda-forge
  font-ttf-source-code-pro           2.038         h77eed37_0                conda-forge
  font-ttf-ubuntu                    0.83          hab24e00_0                conda-forge
  fontconfig                         2.14.1        h77febde_0                conda-forge
  fonts-conda-ecosystem              1             0                         conda-forge
  fonts-conda-forge                  1             0                         conda-forge
  fonttools                          4.38.0        py310h761cc84_1           conda-forge
  fplll                              5.4.2         h6512c63_1                conda-forge
  fpylll                             0.5.7         py310h08e7b9e_1           conda-forge
  freetype                           2.12.1        hbbbf32d_1                conda-forge
  fribidi                            1.0.10        hb9de7d4_0                conda-forge
  future                             0.18.2        pyhd8ed1ab_6              conda-forge
  gap-core                           4.11.1        h7637c83_4                conda-forge
  gap-defaults                       4.11.1        h8af1aa0_4                conda-forge
  gast                               0.5.3         pyhd8ed1ab_0              conda-forge
  gcc_impl_linux-aarch64             10.4.0        h9569200_19               conda-forge
  gcc_linux-aarch64                  10.4.0        h72ad2ee_11               conda-forge
  gettext                            0.21.1        ha18d298_0                conda-forge
  gf2x                               1.3.0         h1b3b3a3_2                conda-forge
  gfan                               0.6.2         h5f589ec_1003             conda-forge
  gfortran_impl_linux-aarch64        10.4.0        hf5786aa_19               conda-forge
  giac                               1.9.0.21      h8f6a60c_0                conda-forge
  giflib                             5.2.1         hb9de7d4_2                conda-forge
  givaro                             4.1.1         h192cbe9_1                conda-forge
  glpk                               5.0           h66325d0_0                conda-forge
  gmp                                6.2.1         h7fd3ca4_0                conda-forge
  gmpy2                              2.1.2         py310h9f74ea4_1           conda-forge
  graphite2                          1.3.13        h7fd3ca4_1001             conda-forge
  gsl                                2.7           h294027d_0                conda-forge
  gxx_impl_linux-aarch64             10.4.0        h9569200_19               conda-forge
  gxx_linux-aarch64                  10.4.0        hb08d869_11               conda-forge
  harfbuzz                           5.3.0         h6f3452c_0                conda-forge
  icu                                70.1          ha18d298_0                conda-forge
  idna                               3.4           pyhd8ed1ab_0              conda-forge
  igraph                             0.9.10        hefb87a8_1                conda-forge
  imagesize                          1.4.1         pyhd8ed1ab_0              conda-forge
  iml                                1.0.5         h9076c59_1003             conda-forge
  importlib-metadata                 5.1.0         pyha770c72_0              conda-forge
  importlib_resources                5.10.1        pyhd8ed1ab_0              conda-forge
  ipykernel                          6.19.1        pyh210e3f2_0              conda-forge
  ipython                            8.7.0         pyh41d4057_0              conda-forge
  ipython_genutils                   0.2.0         py_1                      conda-forge
  ipywidgets                         7.7.2         pyhd8ed1ab_0              conda-forge
  jedi                               0.18.2        pyhd8ed1ab_0              conda-forge
  jinja2                             3.1.2         pyhd8ed1ab_1              conda-forge
  jmol                               14.32.10      h8af1aa0_0                conda-forge
  jpeg                               9e            h9cdd2b7_2                conda-forge
  jsonschema                         4.17.3        pyhd8ed1ab_0              conda-forge
  jupyter_client                     7.4.8         pyhd8ed1ab_0              conda-forge
  jupyter_core                       4.12.0        py310h4c7bcd0_0           conda-forge
  jupyter_server                     1.23.3        pyhd8ed1ab_0              conda-forge
  jupyterlab_pygments                0.2.2         pyhd8ed1ab_0              conda-forge
  jupyterlab_widgets                 1.1.1         pyhd8ed1ab_0              conda-forge
  kernel-headers_linux-aarch64       4.18.0        h5b4a56d_13               conda-forge
  keyutils                           1.6.1         h4e544f5_0                conda-forge
  kiwisolver                         1.4.4         py310h9ceb0a0_1           conda-forge
  krb5                               1.19.3        h750e270_0                conda-forge
  lcalc                              2.0.5         h4e3e9a1_0                conda-forge
  lcms2                              2.14          h5246980_0                conda-forge
  ld_impl_linux-aarch64              2.39          h16cd69b_1                conda-forge
  lerc                               4.0.0         h4de3ea5_0                conda-forge
  libblas                            3.9.0         16_linuxaarch64_openblas  conda-forge
  libbraiding                        1.1           h7fd3ca4_0                conda-forge
  libbrial                           1.2.11        h90c5a80_0                conda-forge
  libbrotlicommon                    1.0.9         h4e544f5_8                conda-forge
  libbrotlidec                       1.0.9         h4e544f5_8                conda-forge
  libbrotlienc                       1.0.9         h4e544f5_8                conda-forge
  libcblas                           3.9.0         16_linuxaarch64_openblas  conda-forge
  libcups                            2.3.3         h0c1ea75_2                conda-forge
  libcurl                            7.86.0        h22f3f83_1                conda-forge
  libdeflate                         1.14          h4e544f5_0                conda-forge
  libedit                            3.1.20191231  he28a2e2_2                conda-forge
  libev                              4.33          h516909a_1                conda-forge
  libffi                             3.4.2         h3557bc0_5                conda-forge
  libflint                           2.9.0         hd3470fa_ntl_100          conda-forge
  libgcc-devel_linux-aarch64         10.4.0        h3c6860a_19               conda-forge
  libgcc-ng                          12.2.0        h607ecd0_19               conda-forge
  libgd                              2.3.3         h1aa4b80_3                conda-forge
  libgfortran-ng                     12.2.0        he9431aa_19               conda-forge
  libgfortran5                       12.2.0        hf695500_19               conda-forge
  libglib                            2.74.1        h01e6fbd_1                conda-forge
  libgomp                            12.2.0        h607ecd0_19               conda-forge
  libhomfly                          1.02r6        hb9de7d4_0                conda-forge
  libhwloc                           2.8.0         hc0facba_1                conda-forge
  libiconv                           1.17          h9cdd2b7_0                conda-forge
  liblapack                          3.9.0         16_linuxaarch64_openblas  conda-forge
  liblapacke                         3.9.0         16_linuxaarch64_openblas  conda-forge
  libnghttp2                         1.47.0        h674c3cc_1                conda-forge
  libnsl                             2.0.0         hf897c2e_0                conda-forge
  libopenblas                        0.3.21        pthreads_h6cb6f83_3       conda-forge
  libpng                             1.6.39        hf9034f9_0                conda-forge
  libsanitizer                       10.4.0        h0e20637_19               conda-forge
  libsodium                          1.0.18        hb9de7d4_1                conda-forge
  libsqlite                          3.40.0        hf9034f9_0                conda-forge
  libssh2                            1.10.0        he5a64b1_3                conda-forge
  libstdcxx-devel_linux-aarch64      10.4.0        h3c6860a_19               conda-forge
  libstdcxx-ng                       12.2.0        hc13a102_19               conda-forge
  libtiff                            4.4.0         hacef7f3_4                conda-forge
  libuuid                            2.32.1        hf897c2e_1000             conda-forge
  libwebp                            1.2.4         hef792ef_0                conda-forge
  libwebp-base                       1.2.4         h4e544f5_0                conda-forge
  libxcb                             1.13          h3557bc0_1004             conda-forge
  libxml2                            2.10.3        h249b6dd_0                conda-forge
  libxslt                            1.1.37        h4871090_0                conda-forge
  libzlib                            1.2.13        h4e544f5_4                conda-forge
  linbox                             1.6.3         h31716a8_7                conda-forge
  lrcalc                             2.1           h4de3ea5_4                conda-forge
  lxml                               4.9.1         py310h141c14b_1           conda-forge
  m4ri                               20140914      h75e8696_1005             conda-forge
  m4rie                              20150908      h75e8696_1001             conda-forge
  make                               4.3           h309ac5b_1                conda-forge
  markupsafe                         2.1.1         py310hdc54845_2           conda-forge
  matplotlib-base                    3.6.2         py310hf92b850_0           conda-forge
  matplotlib-inline                  0.1.6         pyhd8ed1ab_0              conda-forge
  maxima                             5.45.0        haa44c19_3                conda-forge
  memory-allocator                   0.1.2         py310h761cc84_2           conda-forge
  metis                              5.1.0         h7fd3ca4_1006             conda-forge
  mistune                            0.8.4         py310h7cee911_1005        conda-forge
  mpc                                1.2.1         h846f343_0                conda-forge
  mpfi                               1.5.4         h846f343_1001             conda-forge
  mpfr                               4.1.0         h719063d_1                conda-forge
  mpmath                             1.2.1         pyhd8ed1ab_0              conda-forge
  munkres                            1.1.4         pyh9f0ad1d_0              conda-forge
  nauty                              2.7.2         hf897c2e_0                conda-forge
  nbclassic                          0.4.8         pyhd8ed1ab_0              conda-forge
  nbclient                           0.6.8         pyhd8ed1ab_0              conda-forge
  nbconvert                          6.5.3         pyhd8ed1ab_0              conda-forge
  nbconvert-core                     6.5.3         pyhd8ed1ab_0              conda-forge
  nbconvert-pandoc                   6.5.3         pyhd8ed1ab_0              conda-forge
  nbformat                           5.7.0         pyhd8ed1ab_0              conda-forge
  ncurses                            6.3           headf329_1                conda-forge
  nest-asyncio                       1.5.6         pyhd8ed1ab_0              conda-forge
  networkx                           2.8.8         pyhd8ed1ab_0              conda-forge
  notebook                           6.5.2         pyha770c72_1              conda-forge
  notebook-shim                      0.2.2         pyhd8ed1ab_0              conda-forge
  ntl                                11.4.3        h0d7519b_1                conda-forge
  numpy                              1.23.5        py310he617cf3_0           conda-forge
  openblas                           0.3.21        pthreads_h2d9dd7e_3       conda-forge
  openjdk                            17.0.3        h5ee6981_4                conda-forge
  openjpeg                           2.5.0         h9b6de37_1                conda-forge
  openssl                            3.0.7         hb4cce97_1                conda-forge
  packaging                          21.3          pyhd8ed1ab_0              conda-forge
  palp                               2.20          hb9de7d4_0                conda-forge
  pandoc                             2.19.2        h8af1aa0_1                conda-forge
  pandocfilters                      1.5.0         pyhd8ed1ab_0              conda-forge
  pango                              1.50.12       h3f2bcdb_0                conda-forge
  pari                               2.13.3        h05482ea_1_pthread        conda-forge
  pari-galdata                       0.0.20180411  0                         conda-forge
  pari-seadata-small                 0.0.20090618  0                         conda-forge
  parso                              0.8.3         pyhd8ed1ab_0              conda-forge
  pcre2                              10.40         he7b27c6_0                conda-forge
  perl                               5.32.1        2_hf897c2e_perl5          conda-forge
  pexpect                            4.8.0         pyh1a96a4e_2              conda-forge
  pickleshare                        0.7.5         py_1003                   conda-forge
  pillow                             9.2.0         py310hd6d4ca1_3           conda-forge
  pip                                22.3.1        pyhd8ed1ab_0              conda-forge
  pixman                             0.40.0        hb9de7d4_0                conda-forge
  pkg-config                         0.29.2        hb9de7d4_1008             conda-forge
  pkgconfig                          1.5.5         pyhd8ed1ab_4              conda-forge
  pkgutil-resolve-name               1.3.10        pyhd8ed1ab_0              conda-forge
  planarity                          3.0.0.5       hb9de7d4_1002             conda-forge
  ply                                3.11          py_1                      conda-forge
  ppl                                1.2           h984aac9_1006             conda-forge
  pplpy                              0.8.6         py310h5279ff7_1           conda-forge
  primecount                         7.4           hd600fc2_1                conda-forge
  primecountpy                       0.1.0         py310hb15e014_2           conda-forge
  primesieve                         8.0           h4de3ea5_0                conda-forge
  prometheus_client                  0.15.0        pyhd8ed1ab_0              conda-forge
  prompt-toolkit                     3.0.36        pyha770c72_0              conda-forge
  psutil                             5.9.4         py310h761cc84_0           conda-forge
  pthread-stubs                      0.4           hb9de7d4_1001             conda-forge
  ptyprocess                         0.7.0         pyhd3deb0d_0              conda-forge
  pure_eval                          0.2.2         pyhd8ed1ab_0              conda-forge
  pycparser                          2.21          pyhd8ed1ab_0              conda-forge
  pygments                           2.13.0        pyhd8ed1ab_0              conda-forge
  pyopenssl                          22.1.0        pyhd8ed1ab_0              conda-forge
  pyparsing                          3.0.9         pyhd8ed1ab_0              conda-forge
  pyrsistent                         0.19.2        py310hdc54845_0           conda-forge
  pysocks                            1.7.1         pyha2e5f31_6              conda-forge
  python                             3.10.8        hac3cb69_0_cpython        conda-forge
  python-dateutil                    2.8.2         pyhd8ed1ab_0              conda-forge
  python-fastjsonschema              2.16.2        pyhd8ed1ab_0              conda-forge
  python-lrcalc                      2.1           py310h130cc07_4           conda-forge
  python-tzdata                      2022.7        pyhd8ed1ab_0              conda-forge
  python_abi                         3.10          3_cp310                   conda-forge
  pythran                            0.11.0        py310hfd19f87_3           conda-forge
  pytz                               2022.6        pyhd8ed1ab_0              conda-forge
  pytz-deprecation-shim              0.1.0.post0   py310h4c7bcd0_3           conda-forge
  pyzmq                              23.2.1        py310h7c6bb8d_0           conda-forge
  qd                                 2.3.22        h05efe27_1004             conda-forge
  r-base                             4.2.2         h3f2eb09_1                conda-forge
  ratpoints                          2.1.3         h66325d0_1002             conda-forge
  readline                           8.1.2         h38e3740_0                conda-forge
  requests                           2.28.1        pyhd8ed1ab_1              conda-forge
  rpy2                               3.5.6         py310r42h7943a33_0        conda-forge
  rubiks                             20070912      h7fd3ca4_1001             conda-forge
  rw                                 0.9           hf897c2e_0                conda-forge
  sage                               9.7           hd8ed1ab_0                conda-forge
  sagelib                            9.7           py310h04a57a7_1           conda-forge
  sagemath-db-combinatorial-designs  20140630      1                         conda-forge
  sagemath-db-conway-polynomials     0.5.0         h4fd8a4c_1                conda-forge
  sagemath-db-elliptic-curves        0.8.1         hecc5488_0                conda-forge
  sagemath-db-graphs                 20210214      hd8ed1ab_0                conda-forge
  sagemath-db-polytopes              20170220      1                         conda-forge
  sagetex                            3.6.1         pyhd8ed1ab_0              conda-forge
  scipy                              1.9.3         py310hdd6f644_2           conda-forge
  sed                                4.8           ha0d5d3d_0                conda-forge
  send2trash                         1.8.0         pyhd8ed1ab_0              conda-forge
  setuptools                         65.5.1        pyhd8ed1ab_0              conda-forge
  simplegeneric                      0.8.1         py_1                      conda-forge
  singular                           4.2.1.p3      hc324b95_1                conda-forge
  six                                1.16.0        pyh6c4a22f_0              conda-forge
  sniffio                            1.3.0         pyhd8ed1ab_0              conda-forge
  snowballstemmer                    2.2.0         pyhd8ed1ab_0              conda-forge
  soupsieve                          2.3.2.post1   pyhd8ed1ab_0              conda-forge
  sphinx                             4.5.0         pyh6c4a22f_0              conda-forge
  sphinxcontrib-applehelp            1.0.2         py_0                      conda-forge
  sphinxcontrib-devhelp              1.0.2         py_0                      conda-forge
  sphinxcontrib-htmlhelp             2.0.0         pyhd8ed1ab_0              conda-forge
  sphinxcontrib-jsmath               1.0.1         py_0                      conda-forge
  sphinxcontrib-qthelp               1.0.3         py_0                      conda-forge
  sphinxcontrib-serializinghtml      1.1.5         pyhd8ed1ab_2              conda-forge
  sqlite                             3.40.0        h69ca7e5_0                conda-forge
  stack_data                         0.6.2         pyhd8ed1ab_0              conda-forge
  suitesparse                        5.10.1        h1404dd6_1                conda-forge
  symmetrica                         2.0           h7fd3ca4_1007             conda-forge
  sympow                             2.023.6       ha331e0d_2                conda-forge
  sympy                              1.11.1        py310h4c7bcd0_2           conda-forge
  sysroot_linux-aarch64              2.17          h43d7e78_13               conda-forge
  tachyon                            0.99b6        h63ab1d9_1001             conda-forge
  tbb                                2021.7.0      hdd96247_1                conda-forge
  terminado                          0.17.1        pyh41d4057_0              conda-forge
  three.js                           122           hd8ed1ab_2                conda-forge
  threejs-sage                       122           hd8ed1ab_2                conda-forge
  tinycss2                           1.2.1         pyhd8ed1ab_0              conda-forge
  tk                                 8.6.12        hd8af866_0                conda-forge
  tktable                            2.10          hcd05d48_3                conda-forge
  tornado                            6.2           py310hdc54845_1           conda-forge
  traitlets                          5.6.0         pyhd8ed1ab_0              conda-forge
  typing_extensions                  4.4.0         pyha770c72_0              conda-forge
  tzdata                             2022g         h191b570_0                conda-forge
  tzlocal                            4.2           py310h4c7bcd0_2           conda-forge
  unicodedata2                       15.0.0        py310h761cc84_0           conda-forge
  urllib3                            1.26.13       pyhd8ed1ab_0              conda-forge
  wcwidth                            0.2.5         pyh9f0ad1d_2              conda-forge
  webencodings                       0.5.1         py_1                      conda-forge
  websocket-client                   1.4.2         pyhd8ed1ab_0              conda-forge
  wheel                              0.38.4        pyhd8ed1ab_0              conda-forge
  widgetsnbextension                 3.6.1         pyha770c72_0              conda-forge
  xorg-fixesproto                    5.0           h3557bc0_1002             conda-forge
  xorg-inputproto                    2.3.2         h3557bc0_1002             conda-forge
  xorg-kbproto                       1.0.7         h3557bc0_1002             conda-forge
  xorg-libice                        1.0.10        h3557bc0_0                conda-forge
  xorg-libsm                         1.2.3         h965e137_1000             conda-forge
  xorg-libx11                        1.7.2         h3557bc0_0                conda-forge
  xorg-libxau                        1.0.9         h3557bc0_0                conda-forge
  xorg-libxdmcp                      1.1.3         h3557bc0_0                conda-forge
  xorg-libxext                       1.3.4         h3557bc0_1                conda-forge
  xorg-libxfixes                     5.0.3         h3557bc0_1004             conda-forge
  xorg-libxi                         1.7.10        h3557bc0_0                conda-forge
  xorg-libxrender                    0.9.10        h3557bc0_1003             conda-forge
  xorg-libxt                         1.2.1         h3557bc0_2                conda-forge
  xorg-libxtst                       1.2.3         hf897c2e_1002             conda-forge
  xorg-recordproto                   1.14.2        hf897c2e_1002             conda-forge
  xorg-renderproto                   0.11.1        h3557bc0_1002             conda-forge
  xorg-xextproto                     7.3.0         h3557bc0_1002             conda-forge
  xorg-xproto                        7.0.31        h3557bc0_1007             conda-forge
  xsimd                              8.0.5         hd62202e_0                conda-forge
  xz                                 5.2.6         h9cdd2b7_0                conda-forge
  zeromq                             4.3.4         h01db608_1                conda-forge
  zipp                               3.11.0        pyhd8ed1ab_0              conda-forge
  zlib                               1.2.13        h4e544f5_4                conda-forge
  zn_poly                            0.9.2         h719063d_0                conda-forge
  zstd                               1.5.2         hc1e27d5_4                conda-forge

Environment info

__
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/


            environment : base (active)
           env location : /root/micromamba
      user config files : /root/.mambarc
 populated config files :
       libmamba version : 1.1.0
     micromamba version : 1.1.0
           curl version : libcurl/7.86.0 OpenSSL/1.1.1s zlib/1.2.13 libssh2/1.10.0 nghttp2/1.47.0
     libarchive version : libarchive 3.6.1 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       virtual packages : __unix=0=0
                          __linux=5.15.0=0
                          __glibc=2.31=0
                          __archspec=1=aarch64
               channels :
       base environment : /root/micromamba
               platform : linux-aarch64

This warning is not actually correct.

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

There is a warning that pops up that says that if there are issues running sage cli in the virtual environment, then install ipython in the virtual environment. Well, the error doesn't go away even when IPython is installed in the virtual environment.

Note that installing ipython happened like this, not using conda-forge but this higher priority channel...:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ipython-8.12.0             |  py310hca03da5_0         1.1 MB
    ------------------------------------------------------------
                                           Total:         1.1 MB

The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hca03da5_0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            conda-forge/noarch::certifi-2022.12.7~ --> pkgs/main/osx-arm64::certifi-2022.12.7-py310hca03da5_0
  ipython            conda-forge/noarch::ipython-8.12.0-py~ --> pkgs/main/osx-arm64::ipython-8.12.0-py310hca03da5_0

Installed packages

name: myenv
channels:
  - conda-forge
dependencies:
  - sage
  - python=3.10
  - pkgs/main::ipython
  - jupyter
  - pip

Environment info

active environment : myenv
    active env location : /Users/steven/.pyenv/versions/anaconda3-2023.03/envs/myenv
            shell level : 2
       user config file : /Users/steven/.condarc
 populated config files : 
          conda version : 23.3.1
    conda-build version : 3.24.0
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=arm64
                          __osx=12.6=0
                          __unix=0=0
       base environment : /Users/steven/.pyenv/versions/anaconda3-2023.03  (writable)
      conda av data dir : /Users/steven/.pyenv/versions/anaconda3-2023.03/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/steven/.pyenv/versions/anaconda3-2023.03/pkgs
                          /Users/steven/.conda/pkgs
       envs directories : /Users/steven/.pyenv/versions/anaconda3-2023.03/envs
                          /Users/steven/.conda/envs
               platform : osx-arm64
             user-agent : conda/23.3.1 requests/2.28.2 CPython/3.10.10 Darwin/21.6.0 OSX/12.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Sage 9.5: 3D plots broken - share/threejs-sage/r122/three.min.js missing

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

In the terminal

sage: polytopes.cube().plot()
Launched html viewer for Graphics3d Object

Resulting web page is blank.
Viewing page source reveals a hardcode path /Users/mkoeppe/miniconda3/envs/sage-2022-02/share/threejs-sage/r122/three.min.js. This file does not exist

Environment (conda list):

$ conda list
$ conda list
# packages in environment at /Users/mkoeppe/miniconda3/envs/sage-2022-02:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
alabaster                 0.7.12                     py_0    conda-forge
appnope                   0.1.2           py310h2ec42d9_2    conda-forge
arb                       2.21.1               hc148fab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310he24745e_1    conda-forge
arpack                    3.7.0                hefb7bc6_2    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bdw-gc                    8.0.4                h9a9d8cb_0    conda-forge
beniget                   0.4.1              pyhd8ed1ab_0    conda-forge
blas-devel                3.9.0           13_osx64_openblas    conda-forge
bleach                    3.3.1              pyhd8ed1ab_0    conda-forge
brial                     1.2.10             pyh8af1aa0_0    conda-forge
brotli                    1.0.9                h0d85af4_6    conda-forge
brotli-bin                1.0.9                h0d85af4_6    conda-forge
brotlipy                  0.7.0           py310he24745e_1003    conda-forge
bwidget                   1.9.14               h694c41f_1    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.18.1               h0d85af4_0    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cairo                     1.16.0            he01c77b_1009    conda-forge
cctools_osx-64            973.0.1              hb41342b_6    conda-forge
cddlib                    1!0.94m              h0f52abe_0    conda-forge
certifi                   2021.10.8       py310h2ec42d9_1    conda-forge
cffi                      1.15.0          py310hcc37b68_0    conda-forge
charset-normalizer        2.0.11             pyhd8ed1ab_0    conda-forge
clang                     11.1.0               h694c41f_1    conda-forge
clang-11                  11.1.0          default_he082bbe_1    conda-forge
clang_osx-64              11.1.0               hc8532ff_6    conda-forge
clangxx                   11.1.0          default_he082bbe_1    conda-forge
clangxx_osx-64            11.1.0               h2c55bc3_6    conda-forge
cliquer                   1.22                 hbcb3906_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
compiler-rt               11.1.0               h654b07c_0    conda-forge
compiler-rt_osx-64        11.1.0               h8c5fa43_0    conda-forge
cryptography              36.0.1          py310ha82f1d4_0    conda-forge
curl                      7.81.0               hf45b732_0    conda-forge
cvxopt                    1.2.7           py310hfb4135e_1    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cypari2                   2.1.2           py310hc749d29_3    conda-forge
cysignals                 1.11.2          py310h13c92f6_0    conda-forge
cython                    0.29.27         py310hba3363e_0    conda-forge
debugpy                   1.5.1           py310hba3363e_0    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.17.1          py310h2ec42d9_1    conda-forge
dsdp                      5.8               h6e329d1_1203    conda-forge
ecl                       21.2.1               hcd14dc1_1    conda-forge
eclib                     20210625             hdcab1d1_4    conda-forge
ecm                       7.0.4             h343d7f2_1002    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
expat                     2.4.4                he49afe7_0    conda-forge
fflas-ffpack              2.4.3                h026fd7e_2    conda-forge
fftw                      3.3.10          nompi_hf082fe4_102    conda-forge
flintqs                   1.0               ha6586c5_1001    conda-forge
flit-core                 3.6.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.96              h10f422b_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.29.1          py310he24745e_0    conda-forge
fplll                     5.4.1                h1dc45ce_0    conda-forge
fpylll                    0.5.6           py310hd7b656c_1    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
future                    0.18.2          py310h2ec42d9_4    conda-forge
gap-core                  4.11.1               h4855eeb_2    conda-forge
gap-defaults              4.11.1               h694c41f_2    conda-forge
gast                      0.5.3              pyhd8ed1ab_0    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
gf2x                      1.3.0                h0959a2e_1    conda-forge
gfan                      0.6.2             hd793b56_1003    conda-forge
gfortran_impl_osx-64      9.3.0               h9cc0e5e_23    conda-forge
gfortran_osx-64           9.3.0               h18f7dce_15    conda-forge
giac                      1.6.0.47             h6fe0c01_3    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
givaro                    4.1.1                h9bcddcd_2    conda-forge
glpk                      4.65              h0f52abe_1004    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
gmpy2                     2.1.2           py310hf5ec7bd_0    conda-forge
graphite2                 1.3.13            h2e338ed_1001    conda-forge
gsl                       2.7                  h93259b0_0    conda-forge
harfbuzz                  3.3.1                h447b35c_0    conda-forge
icu                       69.1                 he49afe7_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
igraph                    0.9.6                ha5be149_0    conda-forge
imagesize                 1.3.0              pyhd8ed1ab_0    conda-forge
iml                       1.0.5             h64b42ca_1003    conda-forge
importlib-metadata        4.11.0          py310h2ec42d9_0    conda-forge
ipykernel                 6.9.0           py310ha188af9_0    conda-forge
ipython                   7.31.1          py310h2ec42d9_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
jbig                      2.1               h0d85af4_2003    conda-forge
jedi                      0.18.1          py310h2ec42d9_0    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
jmol                      14.32.9              h694c41f_0    conda-forge
jpeg                      9e                   h0d85af4_0    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.1           py310h2ec42d9_1    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.3.2           py310h2fea185_1    conda-forge
krb5                      1.19.2               hcfbf3a7_3    conda-forge
lcalc                     2.0.5                he3dd645_0    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
ld64_osx-64               609                  h6adca69_6    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libblas                   3.9.0           13_osx64_openblas    conda-forge
libbraiding               1.1                  h2e338ed_0    conda-forge
libbrial                  1.2.10               h90380fc_0    conda-forge
libbrotlicommon           1.0.9                h0d85af4_6    conda-forge
libbrotlidec              1.0.9                h0d85af4_6    conda-forge
libbrotlienc              1.0.9                h0d85af4_6    conda-forge
libcblas                  3.9.0           13_osx64_openblas    conda-forge
libclang-cpp11.1          11.1.0          default_he082bbe_1    conda-forge
libcurl                   7.81.0               hf45b732_0    conda-forge
libcxx                    12.0.1               habf9029_1    conda-forge
libdeflate                1.8                  h0d85af4_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libflint                  2.8.4           hd3cc997_ntl_100    conda-forge
libgd                     2.3.3                hb8742e1_1    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran-devel_osx-64  9.3.0               h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libglib                   2.70.2               hf1fb8c0_2    conda-forge
libhomfly                 1.02r6               hc929b4f_0    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.9.0           13_osx64_openblas    conda-forge
liblapacke                3.9.0           13_osx64_openblas    conda-forge
libllvm11                 11.1.0               hd011deb_2    conda-forge
libnghttp2                1.46.0               h6f36284_0    conda-forge
libopenblas               0.3.18          openmp_h3351f45_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libssh2                   1.10.0               h52ee1ee_2    conda-forge
libtiff                   4.3.0                hd146c10_2    conda-forge
libwebp                   1.2.2                h28dabe5_0    conda-forge
libwebp-base              1.2.2                h0d85af4_1    conda-forge
libxml2                   2.9.12               h7e28ab6_1    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
linbox                    1.6.3                h9ed2ecd_6    conda-forge
llvm-openmp               13.0.1               hda6cdc1_0    conda-forge
llvm-tools                11.1.0               hd011deb_2    conda-forge
lrcalc                    1.2               h2e338ed_1000    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
m4ri                      20140914          h3f75d11_1005    conda-forge
m4rie                     20150908          h3f75d11_1001    conda-forge
make                      4.3                  h22f3db7_1    conda-forge
markupsafe                2.0.1           py310he24745e_1    conda-forge
matplotlib-base           3.5.1           py310hfc59cd6_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
maxima                    5.45.0               hd029580_3    conda-forge
memory-allocator          0.1.2           py310he24745e_0    conda-forge
metis                     5.1.0             h2e338ed_1006    conda-forge
mistune                   0.8.4           py310he24745e_1005    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfi                      1.5.4             h52b28e3_1001    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nauty                     2.7.2                h0d85af4_0    conda-forge
nbclient                  0.5.10             pyhd8ed1ab_1    conda-forge
nbconvert                 6.4.2           py310h2ec42d9_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  he49afe7_0    conda-forge
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
notebook                  6.4.8              pyha770c72_0    conda-forge
ntl                       11.4.3               h0ab3c2f_1    conda-forge
numpy                     1.22.2          py310hfbbbacf_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openblas                  0.3.18          openmp_h12da7db_0    conda-forge
openjdk                   11.0.9.1             hcf210ce_1    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openssl                   1.1.1l               h0d85af4_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
palp                      2.20                 hbcb3906_0    conda-forge
pandas                    1.4.1           py310hdd25497_0    conda-forge
pandoc                    2.17.1.1             h694c41f_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.48.10              h056538c_2    conda-forge
pari                      2.13.3          h491590d_1_pthread    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pcre2                     10.37                ha16e1b2_0    conda-forge
perl                      5.32.1          1_h0d85af4_perl5    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    8.4.0           py310h7a4d1b7_0    conda-forge
pip                       22.0.3             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
pkg-config                0.29.2            h31203cd_1008    conda-forge
pkgconfig                 1.5.5           py310h2ec42d9_1    conda-forge
planarity                 3.0.0.5           hbcb3906_1002    conda-forge
ply                       3.11                       py_1    conda-forge
ppl                       1.2               h88b529c_1004    conda-forge
pplpy                     0.8.6           py310h549f3a4_1    conda-forge
primecount                7.2                  he49afe7_1    conda-forge
primecountpy              0.1.0           py310h2fea185_1    conda-forge
primesieve                7.8                  he49afe7_1    conda-forge
prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.27             pyha770c72_0    conda-forge
prompt_toolkit            3.0.27               hd8ed1ab_0    conda-forge
psutil                    5.9.0           py310he24745e_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pynac                     0.7.29          py310hd7b6f9c_2    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.1          py310he24745e_0    conda-forge
pysocks                   1.7.1           py310h2ec42d9_4    conda-forge
python                    3.10.2          h1dd9edd_3_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-tzdata             2021.5             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pythran                   0.10.0          py310h509978a_3    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pytz-deprecation-shim     0.1.0.post0     py310h2ec42d9_1    conda-forge
pyzmq                     22.3.0          py310hcce64c8_1    conda-forge
qd                        2.3.22            h2beb688_1004    conda-forge
r-base                    4.1.2                h2b051ba_0    conda-forge
ratpoints                 2.1.3             h3cb5acd_1002    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
rpy2                      3.4.5           py310r41h81f86ea_3    conda-forge
rubiks                    20070912          h370ebc4_1001    conda-forge
rw                        0.9                  h0d85af4_0    conda-forge
sage                      9.5                  hd8ed1ab_0    conda-forge
sage-docbuild             9.5                      pypi_0    pypi
sage-setup                9.5                      pypi_0    pypi
sagelib                   9.5             py310ha1b8b38_0    conda-forge
sagemath-db-combinatorial-designs 20140630                      0    conda-forge
sagemath-db-conway-polynomials 0.5.0                h033912b_1    conda-forge
sagemath-db-elliptic-curves 0.8.1                hecc5488_0    conda-forge
sagemath-db-graphs        20210214             hd8ed1ab_0    conda-forge
sagemath-db-polytopes     20170220                      0    conda-forge
sagemath-standard         9.5                      pypi_0    pypi
sagetex                   3.6                pyhd8ed1ab_0    conda-forge
scipy                     1.8.0           py310h47774c9_1    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                60.8.2          py310h2ec42d9_0    conda-forge
sigtool                   0.1.3                h57ddcff_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singular                  4.2.0.p3             h6475a08_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
sphinx                    4.4.0              pyh6c4a22f_1    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_1    conda-forge
sqlite                    3.37.0               h23a322b_0    conda-forge
suitesparse               5.10.1               h7aff33d_1    conda-forge
symmetrica                2.0               h2e338ed_1007    conda-forge
sympow                    2.023.6              h9b7075a_2    conda-forge
sympy                     1.9             py310h2ec42d9_1    conda-forge
tachyon                   0.99b6            h2e86ede_1001    conda-forge
tapi                      1100.0.11            h9ce4665_0    conda-forge
tbb                       2021.5.0             h940c156_0    conda-forge
terminado                 0.13.1          py310h2ec42d9_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
three.js                  122                  hd8ed1ab_1    conda-forge
tk                        8.6.11               h5dbffcc_1    conda-forge
tktable                   2.10                 h49f0cf7_3    conda-forge
tornado                   6.1             py310he24745e_2    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
tzlocal                   4.1             py310h2ec42d9_1    conda-forge
unicodedata2              14.0.0          py310he24745e_0    conda-forge
urllib3                   1.26.8             pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.5.2           py310h2ec42d9_1    conda-forge
xsimd                     7.6.0                h940c156_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge
zn_poly                   0.9.2                h0f52abe_0    conda-forge
zstd                      1.5.2                h582d3a0_0    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : sage-2022-02
    active env location : /Users/mkoeppe/miniconda3/envs/sage-2022-02
            shell level : 2
       user config file : /Users/mkoeppe/.condarc
 populated config files : /Users/mkoeppe/.condarc
          conda version : 4.11.0
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages : __osx=10.16=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /Users/mkoeppe/miniconda3  (writable)
      conda av data dir : /Users/mkoeppe/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/mkoeppe/miniconda3/pkgs
                          /Users/mkoeppe/.conda/pkgs
       envs directories : /Users/mkoeppe/miniconda3/envs
                          /Users/mkoeppe/.conda/envs
               platform : osx-64
             user-agent : conda/4.11.0 requests/2.26.0 CPython/3.7.6 Darwin/20.6.0 OSX/10.16
                UID:GID : 502:20
             netrc file : None
           offline mode : False

Update to SageMath 10.0

SageMath 10.0 is out.

• announcement on the sage-release mailing list:
  • https://groups.google.com/g/sage-release/c/BdHjadsnYUc
• SageMath 10.0 release at github:
  • https://github.com/sagemath/sage/releases/tag/10.0

Installing Normaliz causes sagelib downgrade 9.1 -> 9.0

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

Illegal instructions on older processors

Issue: On a machine with Westmere processors (specifically Xeon X5675), I get the following errors in what looks like Linbox:

sage: A = matrix(ZZ, 4, 4, range(16))
sage: A.charpoly()
---------------------------------------------------------------------------
SignalError                               Traceback (most recent call last)
<ipython-input-2-93ceca7ebbc7> in <module>()
----> 1 A.charpoly()

/data/keeling/a/nmd/miniconda3/envs/sage_full/lib/python3.7/site-packages/sage/matrix/matrix_integer_dense.pyx in sage.matrix.matrix_integer_dense.Matrix_integer_dense.charpoly (build/cythonized/sage/matrix/matrix_integer_dense.c:12951)()
   1334         elif algorithm == 'linbox':
   1335             g = (<Polynomial_integer_dense_flint> PolynomialRing(ZZ, names=var).gen())._new()
-> 1336             sig_on()
   1337             linbox_fmpz_mat_charpoly(g.__poly, self._matrix)
   1338             sig_off()

SignalError: Illegal instruction

sage: A.rank()
2
sage: B = A.sparse_matrix()
sage: B.rank()
---------------------------------------------------------------------------
SignalError                               Traceback (most recent call last)
<ipython-input-5-e96f5c5cd86c> in <module>()
----> 1 B.rank()

/data/keeling/a/nmd/miniconda3/envs/sage_full/lib/python3.7/site-packages/sage/matrix/matrix_integer_sparse.pyx in sage.matrix.matrix_integer_sparse.Matrix_integer_sparse.rank (build/cythonized/sage/matrix/matrix_integer_sparse.cpp:7539)()
    607 
    608         if algorithm is None or algorithm == "linbox":
--> 609             r = self._rank_linbox()
    610             self.cache("rank", r)
    611         elif algorithm == "generic":

/data/keeling/a/nmd/miniconda3/envs/sage_full/lib/python3.7/site-packages/sage/matrix/matrix_integer_sparse.pyx in sage.matrix.matrix_integer_sparse.Matrix_integer_sparse._rank_linbox (build/cythonized/sage/matrix/matrix_integer_sparse.cpp:7776)()
    648         cdef size_t r = 0
    649 
--> 650         sig_on()
    651         linbox.rank(r, M[0])
    652         sig_off()

SignalError: Illegal instruction

Environment (conda list): clean install with ``mamba --name=sage_full sage python=3.7``

(sage_full) keeling ~/work $ 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

Sage 9.5

Will this be updated to provide Sage 9.5 ?

@conda-forge-admin, rerender

• I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

Upgrade to 8.1

🤔: These packages are probably not the right version in conda-forge but they should not matter for the conda release.

Base SPKGs that have changed between 7.6 and 8.1 (from git diff 7.6..8.1 build/.)

• 🤔 upgrade configure (212 → 247)

Standard SPKGs that have changed.

• upgrade arb (2.8.1.p1 → 2.11.1.p0) and drop patches/flint_includes.patch
• upgrade BRiAl (0.8.5 → 1.0.1.p1) and patch with patches/BooleConstant_not_const.patch, and some changes in spkg-install
• upgrade conway_polynomials (0.4.p0 → 0.5) and changes to spkg-install
• 🤔 add curl (7.56.1)
• add cypari2 (1.1.3)
• upgrade cysignals (1.3.2 → 1.6.5)
• upgrade cython (0.25.2 → 0.27.2), drop patches/pxi_sys_path.patch,
• upgrade docutils (0.12.p0 → 0.13.1)
• upgrade ecl (16.1.2.p2 → 16.1.2.p4), add patches/flisten-bug.patch, patches/format-directive-limit.patch
• upgrade eclib (20170104 → 20171002)
• upgrade ecm (6.4.4.p0 → 7.0.4.p0), drop patches/asm-align.patch, patches/cygwin.patch.
• upgrade libfplll *fplll (5.0.3rc0 → 5.2.0)
• upgrade fpylll (~0.2.3dev → 0.3.0dev.p0), add patches/ticket-24191.patch (patched in upstream, but only relevant on Cygwin.)
• upgrade GAP (jm5-2015-02-01 → 04jul17), drop patches/gap3_init.patch, patches/gap3_startup.patch and patches/gap3_makefile.patch, and a few changes in spkg-install (I got that one wrong. They did not upgrade gap-4 but gap-3.)
• 🤔 upgrade GAP3(jm5-2015-02-01 → 04jul17), drop patches/gap3_init.patch, patches/gap3_startup.patch and patches/gap3_makefile.patch, and a few changes in spkg-install; we got away without it so far, so GAP-3 does not seem to be necessary.
• upgrade gc (7.2f.p0 → 7.2f.p1)
• 🤔 upgrade gcc (5.4.0 → 7.2.0)
• upgrade gf2x (1.1.p1 → 1.2), add patches/0001-generic_really_is_generic.patch, and drop lots of other patches, disable tuning for SAGE_FAT_BINARY.
• upgrade gfan (0.5.p1 → 0.5.p2), modifies patch to Makefile
• upgrade Giac (1.2.3.25 → 1.2.4.47.p0) which now requires libpng, drop patches/configdotguess.patch, add patches/libpng16.patch, and drop patches/ticket-22315.patch
• upgrade glpk (4.60.p0 → 4.63.p1), add patches/glp_exact_verbosity.patch
• upgrade GSL (2.1.p1 → 2.3)
• upgrade ipython-genutils (0.1.0.p0 → 0.2.0)
• upgrade jupyter-client (4.4.0 → 5.1.0)
• upgrade lcalc (1.23.p14 → 1.23.p15), changes patched Makefile
• upgrade libpng (1.2.51.p0 → 1.6.29), drop patches/pngconf.h.patch, and drop Darwin patches in spkg-install
• upgrade LinBox (1.4,2 → 1.4.2.p1), add patches/linbox-PR50.patch and patches/ticket-23029.patch
• upgrade MPFR (3.1.5 → 3.1.5.p0), add patches/clang_workaround.patch
• upgrade nbformat (4.2.0 → 4.4.0)
• upgrade NTL (10.1.0 → 10.3.0)
• upgrade NumPy (1.11.1.p0 → 1.13.3.p0), add patches/PEP_3141.patch, drop patches/numpy-1.10.1-asarray_conversion.patch, drop patches/numpy-1.11.1-newlib-xlocale.patch.
• upgrade OpenBLAS (0.2.19.p0 → 0.2.20.p1), add patches/88a35ff457f55e527e0e8a503a0dc61976c1846d.patch, modify some build related patches
• upgrade PARI/GP (2.9.1.p2 → 2.10-1280-g88fb5b3.p0), modifies lots of patches; it seems that we can get away with 2.9.4 if we patch away the ellratpoints call (see the recent discussion with the ArchLinux maintainer.)
• add pcre (8.40.p0) [the exact versioin should not matter, and the patches are about Cygwin.]
• upgrade pip (8.1.2.p1 → 9.0.1)
• upgrade planarity (2.2.0 → 3.0.0.5), drop patches/malloc.patch, patches/without_nauty.patch
• upgrade polytopes_db (20120220 → 20170220)
• upgrade prompt_toolkit (1.0.3.p0 → 1.0.9)
• upgrade psutil (4.3.1.p0 → 5.2.0.p0)
• upgrade pygments (2.1.3.p1 → 2.2.0.p0)
• upgrade Pynac (0.7.5 → 0.7.12), drop patches/funcmap-fix.patch
• upgrade Python3 (3.5.1 → 3.6.1.p1)
• 🤔 upgrade R (3.2.4-revised.p0 → 3.4.2.p0), with quite a few patch changes; let's try to get away with an older R. The major version is correct so it might just work™.
• add Requests (2.13.0)
• 🤔 upgrade sagenb_export (2.0.p0 → 3.2); I think we can get away without this. I am not sure but I had the feeling that sagenb (the Sage Notebook?) is going away anyway.
• upgrade SciPy (0.17.1.p0 → 0.19.1)
• upgrade Singular (4.1.0p1 → 4.1.0p3.p0) which drops lots of patches
• upgrade six (1.10.0.p0 → 1.11.0)
• upgrade sphinx (1.4.4.p0 → 1.6.3.p1) with changed patches (not sure what's going on here but I don't want to patch sphinx in conda for Sage)
• upgrade SQLite (autoconf-3130000 → autoconf-3170000)
• upgrade sympow (1.018.1.p11 → 1.018.1.p12), adds patches/initialize-tacks.patch
• upgrade sympy (1.0.p1 → 1.1.1), replaces undeffun patch.
• upgrade tachyon (0.98.9.p5 → 0.98.9.p6)
• add typing (3.6.1)
• add Yasm (1.3.0)
• upgrade zeromq (4.0.5 → 4.0.5.p1) with build changes only
• upgrade zlib (1.2.8.p0 → 1.2.11)

Optional SPKGs that have changed.
😞: Proper support for optional packages won't come before Sage 8.3 with the inclusion of https://trac.sagemath.org/ticket/20382. These packages are probably not present in conda-forge but it does not matter at the moment as they would not be detected by Sage anyway.

• 🤔 upgrade autotools (20141105 → 20141105.p0)
• upgrade cmake (3.2.3 → 3.8.1) with patches/osx10.10.patch for OS X and some minor changes in spkg-install.
• 😞 upgrade Coxeter (3.0_beta2 → 3.1.sage) ?
• 😞 upgrade CryptoMiniSat (2.9.6 → 5.0.1) and apply patches/osx_install_nameQA.patch, and changes in spkg-install (conda-forge/staged-recipes#5185, msoos/cryptominisat#459)
• 😞 add Deformation (d05941b)
• 😞 upgrade dot2tex (2.9.0.p1 → 2.9.0.p2), and add graphviz as a requirement in spkg-install
• 😞 upgrade FriCAS (1.2.7 → 1.3.2), drop patches/uffi.patch,
• 😞 upgrade gambit (14.1.0 → 15.1.1), add patches/b91115633dbf6f64745fda2db7fbb83f918dd500.patch
• 😞 add Jupyter kernel for GAP (0.9)
• 😞 upgrade giacpy (0.6 → 0.6.6)
• upgrade GMP (5.1.3 → 6.1.2)
• 😞 upgrade gmpy2 (2.0.8 → 2.0.8.p0), add patches/no_set_memory_functions.patch
• 😞 upgrade libhomfly (1.0 → 1.0r2)
• 😞 upgrade Meataxe (2.4.24.p1 → 2.4.24.p3), add patches/TrueRowSize.patch, patches/mtxdirs.patch
• 😞 add Mpfrcx (0.4.2)
• 😞 upgrade MPIR (2.7.2.p0 → 3.0.0-644faf502c56f97d9accd301965fc57d6ec70868), drop patches/PR185.patch, and some changes to spkg-install
• 😞 upgrade normaliz (3.1.4 → 3.2.1), and add /patches/22684_cone_reduce_memory_usage.patch
• 😞 upgrade OpenSSL (1.0.2j → 1.0.2m)
• 😞 upgrade Ore_algebra (0.2.p0 → 0.3)
• 😞 upgrade pynormaliz (1.0 → 1.5)
• 😞 upgrade pysingular (0.9.1 → 0.9.5)
• 😞 upgrade Python (2.7.13.p0 → 2.7.14.p2), add patches/linux_linking_issue_25229.patch
• 😞 upgrade rst2ipynb (0.2.1 → 0.2.2.p0), adds patches/check-pandoc.patch
• 😞 upgrade sagenb (0.13 → 1.0.1)
• 😞 add SIP (4.18)
• 😞 add SIROCCO (2.0)

Experimental SPKGs that have changed.

• 😞 upgrade polymake (3.0r2 → 3.1), add patches/fix-compilation-with-gcc7.patch
• 😞 upgrade scipoptsuite (3.2.1 → 4.0.0), with many changed patches

New runtime dependencies:

• cypari is now a standard SPKG
• fplll is now a standard SPKG
• pcre is now a standard SPKG
• Requests is now a standard SPKG

New build-time dependencies:

• sympy (doc build dependency)
• typing (doc build dependency)

Remove unnecessary packages from runtime

For eg: I think boost-cpp is unneeded. @saraedum, is that right?

Can't install via conda or mamba on Windows

Issue: Can't install via conda nor mamba on my Windows PC. Recently installed it on Mac yesterday (i'll check if can install it again today).

I tried the following commands:

conda config --add channels conda-forge
conda install sage
conda install sage -c conda-forge
conda create -n sage sage
conda create -n sage sage -c conda-forge
mamba install sage
mamba install sage -c conda-forge
mamba create -n sage sage
mamba create -n sage sage -c conda-forge

And I'm always met with either

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - sage

Current channels:

  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

or

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        Supported by @QuantStack

        GitHub:  https://github.com/QuantStack/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Getting  conda-forge win-64
Getting  conda-forge noarch
Getting  pkgs/main win-64
Getting  pkgs/main noarch
Getting  pkgs/r win-64
Getting  pkgs/r noarch
Getting  pkgs/msys2 win-64
Getting  pkgs/msys2 noarch

Looking for: ['sage']

65006 packages in https://conda.anaconda.org/conda-forge/win-64
20907 packages in https://conda.anaconda.org/conda-forge/noarch
5023 packages in https://repo.anaconda.com/pkgs/r/noarch
1122 packages in https://repo.anaconda.com/pkgs/main/noarch
13807 packages in https://repo.anaconda.com/pkgs/main/win-64
4224 packages in https://repo.anaconda.com/pkgs/r/win-64
471 packages in https://repo.anaconda.com/pkgs/msys2/win-64
0 packages in https://repo.anaconda.com/pkgs/msys2/noarch
Encountered problems while solving.
Problem: nothing provides requested sage

Environment (conda list):

C:\Users\dkhodabakhsh>conda list
# packages in environment at C:\Users\dkhodabakhsh\AppData\Local\Continuum\miniconda3:
#
# Name                    Version                   Build  Channel
ca-certificates           2019.11.28           hecc5488_0    conda-forge
certifi                   2019.11.28               py37_0    conda-forge
cffi                      1.13.2           py37hb32ad35_0    conda-forge
chardet                   3.0.4                 py37_1003    conda-forge
conda                     4.8.0                    py37_1    conda-forge
conda-package-handling    1.6.0            py37h2fa13f4_1    conda-forge
console_shortcut          0.1.1                         3
cryptography              2.8              py37hb32ad35_1    conda-forge
idna                      2.8                   py37_1000    conda-forge
libsolv                   0.7.10               h1a1b453_0    conda-forge
mamba                     0.1.0            py37h1ad3211_2    conda-forge
menuinst                  1.4.16                   py37_0    conda-forge
openssl                   1.1.1d               hfa6e2cd_0    conda-forge
pip                       19.3.1                   py37_0    conda-forge
powershell_shortcut       0.0.1                         2
pycosat                   0.6.3           py37hfa6e2cd_1002    conda-forge
pycparser                 2.19                     py37_1    conda-forge
pyopenssl                 19.1.0                   py37_0    conda-forge
pysocks                   1.7.1                    py37_0    conda-forge
python                    3.7.6                h5b45d93_2    conda-forge
pywin32                   225              py37hfa6e2cd_0    conda-forge
requests                  2.22.0                   py37_1    conda-forge
ruamel_yaml               0.15.80         py37hfa6e2cd_1000    conda-forge
setuptools                45.0.0                   py37_1    conda-forge
six                       1.14.0                   py37_0    conda-forge
sqlite                    3.30.1               hfa6e2cd_0    conda-forge
tqdm                      4.41.1                     py_0    conda-forge
urllib3                   1.25.7                   py37_0    conda-forge
vc                        14.1                 h0510ff6_4
vs2015_runtime            14.16.27012          hf0eaf9b_1
wheel                     0.33.6                   py37_0    conda-forge
win_inet_pton             1.1.0                    py37_0    conda-forge
wincertstore              0.2                   py37_1003    conda-forge
yaml                      0.2.2                hfa6e2cd_1    conda-forge
zlib                      1.2.11            h2fa13f4_1006    conda-forge

Details about conda and system ( conda info ):

C:\Users\dkhodabakhsh>conda info

     active environment : None
       user config file : C:\Users\dkhodabakhsh\.condarc
 populated config files : C:\Users\dkhodabakhsh\.condarc
          conda version : 4.8.0
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages :
       base environment : C:\Users\dkhodabakhsh\AppData\Local\Continuum\miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\dkhodabakhsh\AppData\Local\Continuum\miniconda3\pkgs
                          C:\Users\dkhodabakhsh\.conda\pkgs
                          C:\Users\dkhodabakhsh\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\dkhodabakhsh\AppData\Local\Continuum\miniconda3\envs
                          C:\Users\dkhodabakhsh\.conda\envs
                          C:\Users\dkhodabakhsh\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.8.0 requests/2.22.0 CPython/3.7.6 Windows/10 Windows/10.0.18362
          administrator : False
             netrc file : None
           offline mode : False

Recreation of environment yml file fails due sagemath-standard requirements

• I read the conda-forge documentation and could not find the solution for my problem there.

Hi you all,
thanks a lot in advance for taking the time to read my issue!

Issue:

I try to export a conda environment with sagelib in it to a yml file.
The installation of sagelib works fine, but when i try to recreate the environment from the exported yml file, the package sagemath-standard is causing trouble as the requirements for this package cannot be installed, specifically the rpy2 package.

So if i understand correctly it could install sagelib properly also with the pip depenency sagemath-standard?
The recreation of the environment fails, also when i try to install sagemath-standard manually i get the same error message (therefore i am surprised it could be installed as dependency of sagelib).

conda create -n sage python=3.8.12
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install -c conda-forge sagelib
conda env export > sage.yml
conda env create -f sage.yml

Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.11.0

Please update conda by running

    $ conda update -n base -c defaults conda


Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/home/sgriesmayr/.conda/envs/sage_imported/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/sgriesmayr/condaenv.ocxjux47.requirements.txt']
Pip subprocess output:
Requirement already satisfied: sage-docbuild==9.5 in ./.conda/envs/sage_imported/lib/python3.8/site-packages (from -r /home/sgriesmayr/condaenv.ocxjux47.requirements.txt (line 1)) (9.5)
Requirement already satisfied: sage-setup==9.5 in ./.conda/envs/sage_imported/lib/python3.8/site-packages (from -r /home/sgriesmayr/condaenv.ocxjux47.requirements.txt (line 2)) (9.5)
Requirement already satisfied: sagemath-standard==9.5 in ./.conda/envs/sage_imported/lib/python3.8/site-packages (from -r /home/sgriesmayr/condaenv.ocxjux47.requirements.txt (line 3)) (9.5)
Collecting sphinx
  Using cached Sphinx-4.4.0-py3-none-any.whl (3.1 MB)

........

Collecting rpy2<3.4,>=3.3
  Using cached rpy2-3.3.6.tar.gz (179 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'

Pip subprocess error:
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [4 lines of output]
      cffi mode: CFFI_MODE.ANY
      /home/sgriesmayr/.conda/envs/sage_imported/lib/python3.8/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
        warnings.warn(
      Error: rpy2 in API mode cannot be built without R in the PATH or R_HOME defined. Correct this or force ABI mode-only by defining the environment variable RPY2_CFFI_MODE=ABI
      [end of output]

Environment (conda list):

$ conda list
# packages in environment at /home/sgriesmayr/.conda/envs/sage:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
arb                       2.22.1               hbbd85db_0    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
bdw-gc                    8.0.6                h4bd325d_0    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cddlib                    1!0.94m              h9202a9a_0    conda-forge
cliquer                   1.22                 h36c2ea0_0    conda-forge
cypari2                   2.1.2            py38hb44a72f_4    conda-forge
cysignals                 1.11.2           py38h4888d1d_0    conda-forge
cython                    0.29.28          py38h709712a_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
ecl                       21.2.1               h9d73b02_2    conda-forge
eclib                     20210625             h52f5ea4_4    conda-forge
ecm                       7.0.4             h9202a9a_1002    conda-forge
expat                     2.4.6                h27087fc_0    conda-forge
fflas-ffpack              2.4.3                h912ac81_2    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.96              ha180cfb_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
future                    0.18.2           py38h578d9bd_4    conda-forge
gap-core                  4.11.1               h1725ef4_3    conda-forge
gf2x                      1.3.0                h75e9656_1    conda-forge
giac                      1.6.0.47             haa4998e_4    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
givaro                    4.1.1                h192cbe9_1    conda-forge
glpk                      4.65              h9202a9a_1004    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.2            py38h8384b0a_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
icu                       69.1                 h9c3ff4c_0    conda-forge
igraph                    0.9.6                ha184e22_0    conda-forge
iml                       1.0.5             hd75c201_1003    conda-forge
ipython                   7.31.1           py38h578d9bd_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.1           py38h578d9bd_0    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h7f98852_0    conda-forge
jupyter_core              4.9.2            py38h578d9bd_0    conda-forge
krb5                      1.19.2               h48eae69_3    conda-forge
lcalc                     2.0.5                h8cd7e2e_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           13_linux64_openblas    conda-forge
libbraiding               1.1                  h58526e2_0    conda-forge
libbrial                  1.2.10               hb0536f6_0    conda-forge
libcblas                  3.9.0           13_linux64_openblas    conda-forge
libcurl                   7.81.0               h494985f_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflint                  2.8.4           hd3cd37b_ntl_100    conda-forge
libgcc-ng                 11.2.0              h1d223b6_12    conda-forge
libgd                     2.3.3                h3cfcdeb_1    conda-forge
libgfortran-ng            11.2.0              h69a702a_12    conda-forge
libgfortran5              11.2.0              h5c6108e_12    conda-forge
libgomp                   11.2.0              h1d223b6_12    conda-forge
libhomfly                 1.02r6               h36c2ea0_0    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           13_linux64_openblas    conda-forge
liblapacke                3.9.0           13_linux64_openblas    conda-forge
libnghttp2                1.47.0               he49606f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libssh2                   1.10.0               ha35d2d1_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_12    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxml2                   2.9.12               h885dcf4_1    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
linbox                    1.6.3                hf8a3fca_6    conda-forge
lrcalc                    1.2               h58526e2_1000    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
m4ri                      20140914          h7ca028e_1005    conda-forge
m4rie                     20150908          h7ca028e_1001    conda-forge
markupsafe                2.1.0            py38h0a891b7_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
memory-allocator          0.1.2            py38h497a2fe_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mpc                       1.2.1                h9f54685_0    conda-forge
mpfi                      1.5.4             h9f54685_1001    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
nauty                     2.7.2                h7f98852_0    conda-forge
ncurses                   6.3                  h9c3ff4c_0    conda-forge
ntl                       11.4.3               hef3c4d3_1    conda-forge
numpy                     1.22.2           py38h6ae9a64_0    conda-forge
openssl                   3.0.0                h7f98852_2    conda-forge
pari                      2.13.3          he2feae2_1_pthread    conda-forge
pari-galdata              0.0.20180411                  0    conda-forge
pari-seadata-small        0.0.20090618                  0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       22.0.3             pyhd8ed1ab_0    conda-forge
planarity                 3.0.0.5           h36c2ea0_1002    conda-forge
ppl                       1.2               h8c76519_1004    conda-forge
pplpy                     0.8.6            py38h87e0038_1    conda-forge
primecount                7.2                  hcb278e6_1    conda-forge
primecountpy              0.1.0            py38h1fd1430_1    conda-forge
primesieve                7.8                  h9c3ff4c_1    conda-forge
prompt-toolkit            3.0.27             pyha770c72_0    conda-forge
psutil                    5.9.0            py38h497a2fe_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pynac                     0.7.29           py38he7f92b8_2    conda-forge
python                    3.8.12          h0744224_3_cpython    conda-forge
python_abi                3.8                      2_cp38    conda-forge
ratpoints                 2.1.3             h445213a_1002    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
rw                        0.9                  h7f98852_0    conda-forge
sage-docbuild             9.5                      pypi_0    pypi
sage-setup                9.5                      pypi_0    pypi
sagelib                   9.5              py38hd903835_2    conda-forge
sagemath-standard         9.5                      pypi_0    pypi
setuptools                60.9.3           py38h578d9bd_0    conda-forge
singular                  4.2.0.p3             h949c820_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.37.0               h9cd32fc_0    conda-forge
suitesparse               5.10.1               h9e50725_1    conda-forge
symmetrica                2.0               h58526e2_1007    conda-forge
tbb                       2021.5.0             h4bd325d_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zn_poly                   0.9.2                h9202a9a_0    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : sage
    active env location : /home/sgriesmayr/.conda/envs/sage
            shell level : 2
       user config file : /home/sgriesmayr/.condarc
 populated config files : /home/sgriesmayr/.condarc
          conda version : 4.10.3
    conda-build version : 3.21.5
         python version : 3.9.7.final.0
       virtual packages : __cuda=11.4=0
                          __linux=5.4.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/anaconda3  (read only)
      conda av data dir : /opt/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          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
          package cache : /opt/anaconda3/pkgs
                          /home/sgriesmayr/.conda/pkgs
       envs directories : /home/sgriesmayr/.conda/envs
                          /opt/anaconda3/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.7 Linux/5.4.0-99-generic ubuntu/20.04.3 glibc/2.31
                UID:GID : 1008:1008
             netrc file : None
           offline mode : False

Runtime dependencies should be at least the version that Sage's SPKGs provide

Sage Notebook does not open properly when installed using Conda

Issue:

So it seems that when installing sage with conda through conda-forge, the dependencies for the sage notebook environment do not come along for the ride.

Typing : sage -n sagenb (to start the sage default notebook) yields the following error:

Please wait while the old SageNB Notebook server starts...
Traceback (most recent call last):
  File "/home/zeru/miniconda3/envs/sage/bin/sage-notebook", line 268, in <module>
    launcher(unknown)
  File "/home/zeru/miniconda3/envs/sage/bin/sage-notebook", line 69, in __init__
    from sagenb.notebook.notebook_object import notebook
ImportError: No module named sagenb.notebook.notebook_object

Additionally, in /miniconda3/envs/sage/bin there only seems to be a single py script, sage-notebook.py for the execution of the notebook.

An additional error that comes about when attempting to use other notebook back-ends. default and export yield 404 pages on local host and no other options. the IPython and Jupyter options work fine.

strangely enough, the same command integrate does not work for simple cases in either of the working notebooks, or of the shell, for simple integrals like integrate(x^2,x).
integralerror.txt

I am not a programmer of a high calibur, as I am a mere physicist, but i thought here would be the appropriate place to document this bug.

Let me know if i could help debug this nasty mess.

Environment (

``` alabaster 0.7.11 py_3 conda-forge appdirs 1.4.3 py_1 conda-forge arb 2.13.0 hb705a9b_1 conda-forge asn1crypto 0.24.0 py_1 conda-forge attrs 18.1.0 py_1 conda-forge automat 0.7.0 py27_0 conda-forge babel 2.6.0 py_1 conda-forge backports 1.0 py27_1 conda-forge backports.functools_lru_cache 1.5 py27_0 conda-forge backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge backports_abc 0.5 py27_0 conda-forge bdw-gc 7.6.4 h2d50403_2 conda-forge blas 1.1 openblas conda-forge bleach 2.1.3 py_0 conda-forge boost-cpp 1.67.0 h3a22d5f_0 conda-forge brial 1.2.3 py_2 conda-forge bzip2 1.0.6 1 conda-forge ca-certificates 2018.4.16 0 conda-forge cairo 1.14.12 h77bcde2_0 cddlib 1!0.94i h16a7912_1 conda-forge certifi 2018.4.16 py27_0 conda-forge cffi 1.11.5 py27_0 conda-forge chardet 3.0.4 py_1 conda-forge cliquer 1.21 0 conda-forge configparser 3.5.0 py27_0 conda-forge constantly 15.1.0 py_0 conda-forge cryptography 2.2.1 py27hdffb7b8_1 conda-forge curl 7.60.0 0 conda-forge cvxopt 1.2.0 py27_blas_openblash9c03b7d_202 [blas_openblas] conda-forge cycler 0.10.0 py_1 conda-forge cypari2 1.1.4 py27h16a7912_2 conda-forge cysignals 1.7.1 py27h470a237_0 conda-forge cython 0.28.4 py27hfc679d8_0 conda-forge dbus 1.13.0 h3a4f0e9_0 conda-forge decorator 4.3.0 py_0 conda-forge docutils 0.14 py27_0 conda-forge dsdp 5.8 blas_openblash470a237_201 [blas_openblas] conda-forge ecl 16.1.3 h0b9cf6d_5 conda-forge eclib 20171219 h075c78f_1 conda-forge ecm 7.0.4 h16a7912_2 conda-forge entrypoints 0.2.3 py27_1 conda-forge enum34 1.1.6 py27_1 conda-forge expat 2.2.5 hfc679d8_1 conda-forge fastcache 1.0.2 py27_0 conda-forge fflas-ffpack 2.3.2 blas_openblashb06058e_1 [blas_openblas] conda-forge fftw 3.3.8 h470a237_0 conda-forge flintqs 1.0 0 conda-forge fontconfig 2.12.6 0 conda-forge fplll 5.2.0 h075c78f_1 conda-forge fpylll 0.3.0dev py27h075c78f_2 conda-forge freetype 2.8.1 0 conda-forge functools32 3.2.3.2 py27_2 conda-forge future 0.16.0 py27_0 conda-forge gap 4.8.6 hca56440_3 conda-forge gf2x 1.2 hfc679d8_2 conda-forge gfan 0.5 h0eace8b_1 conda-forge giac 1.4.9.57 blas_openblashb294cb5_3 [blas_openblas] conda-forge giflib 5.1.4 h470a237_0 conda-forge givaro 4.0.4 h0eace8b_1 conda-forge glib 2.53.6 h5d9569c_2 glpk 4.65 h16a7912_1 conda-forge gmp 6.1.2 hfc679d8_0 conda-forge gmpy2 2.0.8 py27_0 conda-forge graphite2 1.3.11 hfc679d8_0 conda-forge gsl 2.2.1 blas_openblas_4 [blas_openblas] conda-forge gst-plugins-base 1.12.4 h33fb286_0 gstreamer 1.12.4 hb53b477_0 harfbuzz 1.7.6 hc5b324e_0 html5lib 1.0.1 py_0 conda-forge hyperlink 17.3.1 py_0 conda-forge icu 58.2 hfc679d8_0 conda-forge idna 2.7 py_1 conda-forge imagesize 1.0.0 py_1 conda-forge iml 1.0.5 blas_openblash905a843_1 [blas_openblas] conda-forge incremental 17.5.0 py_0 conda-forge ipaddress 1.0.22 py_1 conda-forge ipykernel 4.8.2 py27_0 conda-forge ipython 5.7.0 py27_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.2.1 py27_1 conda-forge jinja2 2.10 py27_0 conda-forge jmol 14.29.15 1 conda-forge jpeg 9c h470a237_0 conda-forge jsonschema 2.6.0 py27_1 conda-forge jupyter_client 5.2.3 py_1 conda-forge jupyter_core 4.4.0 py_0 conda-forge kiwisolver 1.0.1 py27_1 conda-forge krb5 1.14.6 0 conda-forge lcalc 1.23 heb735ee_1 conda-forge libbrial 1.2.3 hafa9fcd_2 conda-forge libffi 3.2.1 3 conda-forge libflint 2.5.2 heb735ee_2 conda-forge libgap 4.8.6 hb705a9b_1 conda-forge libgcc 7.2.0 h69d50b8_2 libgcc-ng 7.2.0 hdf63c60_3 libgd 2.2.5 3 conda-forge libgfortran 3.0.0 1 libiconv 1.15 h470a237_1 conda-forge libpng 1.6.34 ha92aebf_1 conda-forge libsodium 1.0.16 0 conda-forge libssh2 1.8.0 h5b517e9_2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 libtiff 4.0.9 he6b73bb_1 conda-forge libwebp 0.5.2 7 conda-forge libxcb 1.13 h470a237_1 conda-forge libxml2 2.9.8 h422b904_2 conda-forge linbox 1.5.2 hb3e9661_2 conda-forge lrcalc 1.2 0 conda-forge m4ri 20140914 0 conda-forge m4rie 20150908 0 conda-forge markupsafe 1.0 py27_0 conda-forge matplotlib 2.2.2 py27_1 conda-forge maxima 5.39.0 h0b9cf6d_3 conda-forge metis 5.1.0 3 conda-forge mistune 0.8.3 py27_1 conda-forge mpc 1.1.0 hb705a9b_6 conda-forge mpfi 1.5.3 hb705a9b_1 conda-forge mpfr 4.0.1 h16a7912_0 conda-forge mpmath 1.0.0 py_0 conda-forge nauty 2.6r7 0 conda-forge nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py27_0 conda-forge ncurses 5.9 10 conda-forge networkx 1.11 py27_0 conda-forge notebook 5.5.0 py27_0 conda-forge ntl 10.3.0 1 conda-forge numpy 1.14.5 py27_blas_openblashd3ea46f_201 [blas_openblas] conda-forge olefile 0.45.1 py_1 conda-forge openblas 0.2.20 8 conda-forge openjdk 8.0.144 zulu8.23.0.3_1 conda-forge openssl 1.0.2o 0 conda-forge packaging 17.1 py_0 conda-forge palp 2.1 0 conda-forge pandoc 2.2.1 0 conda-forge pandocfilters 1.4.2 py27_0 conda-forge pango 1.40.14 0 conda-forge pari 2.9.5 pl526h787e8ac_1 conda-forge path.py 11.0.1 py_0 conda-forge pathlib2 2.3.2 py27_0 conda-forge pcre 8.39 0 conda-forge perl 5.26.2 h470a237_0 conda-forge pexpect 4.6.0 py27_0 conda-forge pickleshare 0.7.4 py27_0 conda-forge pillow 4.3.0 py27_2 conda-forge pip 9.0.3 py27_0 conda-forge pixman 0.34.0 2 conda-forge pkg-config 0.29.2 1 conda-forge pkgconfig 1.3.1 py27_0 conda-forge planarity 3.0.0.5 0 conda-forge ppl 1.2 0 conda-forge prompt_toolkit 1.0.15 py27_0 conda-forge psutil 5.4.6 py27_0 conda-forge pthread-stubs 0.4 h470a237_1 conda-forge ptyprocess 0.6.0 py27_0 conda-forge pyasn1 0.4.3 py_0 conda-forge pyasn1-modules 0.2.1 py_0 conda-forge pycparser 2.18 py27_0 conda-forge pycrypto 2.6.1 py27_1 conda-forge pygments 2.2.0 py_1 conda-forge pyhamcrest 1.9.0 py27_1 conda-forge pynac 0.7.17 py27h075c78f_1 conda-forge pyopenssl 18.0.0 py27_0 conda-forge pyparsing 2.2.0 py_1 conda-forge pyqt 5.6.0 py27h8210e8a_6 conda-forge pysocks 1.6.8 py27_1 conda-forge python 2.7.14 ha6fc286_23 python-dateutil 2.7.3 py_0 conda-forge pytz 2018.5 py_0 conda-forge pyzmq 17.0.0 py27_4 conda-forge qd 2.3.17 h26a2512_2 conda-forge qt 5.6.2 hd25b39d_14 r-base 3.4.1 4 conda-forge ratpoints 2.1.3 h16a7912_2 conda-forge readline 7.0 0 conda-forge requests 2.19.1 py_1 conda-forge rpy2 2.8.5 py27r3.4.1_0 conda-forge rubiks 20070912 0 conda-forge rw 0.7 1 conda-forge sage 8.2 py27_2 conda-forge sagelib 8.2 py27_blas_openblash4416362_3 [blas_openblas] conda-forge sagemath-db-combinatorial-designs 20140630 0 conda-forge sagemath-db-conway-polynomials 0.5.p0 py27_0 conda-forge sagemath-db-elliptic-curves 0.8 1 conda-forge sagemath-db-graphs 20161026 0 conda-forge sagemath-db-polytopes 20170220 0 conda-forge scandir 1.7 py27_0 conda-forge scipy 1.1.0 py27_blas_openblas_200 [blas_openblas] conda-forge send2trash 1.5.0 py_0 conda-forge service_identity 17.0.0 py_0 conda-forge setuptools 40.0.0 py27_0 conda-forge simplegeneric 0.8.1 py_1 conda-forge singledispatch 3.4.0.3 py27_0 conda-forge singular 4.1.0.p3 h1e9d69d_2 conda-forge sip 4.18 py27_1 conda-forge six 1.11.0 py27_1 conda-forge snowballstemmer 1.2.1 py_1 conda-forge sphinx 1.7.5 py27_0 conda-forge sphinxcontrib-websupport 1.0.1 py27_0 conda-forge sqlite 3.23.1 h2d50403_0 conda-forge ssl_match_hostname 3.5.0.1 py27_1 conda-forge subprocess32 3.5.2 py27_0 conda-forge suitesparse 4.5.6 blas_openblas_200 [blas_openblas] conda-forge symmetrica 2.0 0 conda-forge sympow 1.018.1 h470a237_2 conda-forge sympy 1.1.1 py27_0 conda-forge tachyon 0.99b6 0 conda-forge tbb 2018_20171205 0 conda-forge terminado 0.8.1 py27_0 conda-forge testpath 0.3.1 py27_0 conda-forge tk 8.6.7 0 conda-forge tornado 4.5.3 py27_0 conda-forge traitlets 4.3.2 py27_0 conda-forge twisted 18.4.0 py27h470a237_0 conda-forge typing 3.6.4 py27_2 conda-forge urllib3 1.23 py27_0 conda-forge wcwidth 0.1.7 py_1 conda-forge webencodings 0.5 py27_0 conda-forge wheel 0.31.1 py27_0 conda-forge widgetsnbextension 3.2.1 py27_0 conda-forge xorg-libxau 1.0.8 h470a237_5 conda-forge xorg-libxdmcp 1.1.2 h470a237_6 conda-forge xz 5.2.3 0 conda-forge zeromq 4.2.5 hfc679d8_3 conda-forge zlib 1.2.11 h470a237_3 conda-forge zn_poly 0.9 h16a7912_2 conda-forge zope.interface 4.5.0 py27h470a237_0 conda-forge ``` ):

Details about conda and system ( conda info ):

     active environment : sage
    active env location : /home/zeru/miniconda3/envs/sage
            shell level : 1
       user config file : /home/zeru/.condarc
 populated config files : /home/zeru/.condarc
          conda version : 4.5.6
    conda-build version : not installed
         python version : 3.6.5.final.0
       base environment : /home/zeru/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/zeru/miniconda3/pkgs
                          /home/zeru/.conda/pkgs
       envs directories : /home/zeru/miniconda3/envs
                          /home/zeru/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.6 requests/2.19.1 CPython/3.6.5 Linux/4.15.0-23-generic ubuntu/18.04 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Package Sage optional packages

• lrslib - conda-forge/staged-recipes#9133
• polymake (actually still an 'experimental' package)
• topcom
• 4ti2 - conda-forge/staged-recipes#8951
• latte_int - conda-forge/staged-recipes#8959
• pynormaliz
• sage_numerical_backends_coin

Installation Failure on Windows 10 with Conda

I was just following the installation guide

When I run
conda create -n sage sage python=3.9
I get the following output:

Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
Examining conflict for sage:  75%|██████████████████████████████████████████████████████▊                  | 3/4 [00:15<00:05,  5.60s/it]|failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for:
python=3.9
sage -> python[version='>=3.6|>=3.7']
sage -> alabaster[version='>=0.7.12'] -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0|3.4.*|>=3.11,<3.12.0a0|>=3.5|>=3.8|>=2.7|>=3|>=3.3|>=3.6.1']The following specifications were found to be incompatible with your system:

  - feature:/win-64::__win==0=0
  - feature:|@/win-64::__win==0=0
  - sage -> ipykernel[version='>=6.6.0,<7'] -> __linux
  - sage -> ipykernel[version='>=6.6.0,<7'] -> __win

Your installed version is: 0

I have tried with Python 3.9, 3.10 and 3.11. I am not sure if I am missing something here.

conda: Sage documentation not installed

Issue:

I installed Sage using mamba, the Sage documentation does not seem to be available. As a new user, I have not been able to find a solution. I suggest that document installation should be by default, or at-least a well explained option. I used this guide for installation: Sage Install Guide>Install from conda-forge

% mamba env create --file ./environment.yml

I always use an environment.yml to manage conda environments. I had already installed mamba into my base environment.

name: SageMath
channels:
  - conda-forge
  - anaconda
  - defaults
dependencies:
  - conda-forge::sage
  - conda-forge::mamba
  - anaconda::python>=3.7
  - nodejs
  - pip

Opening a sage notebook server %sage -n jupyter . I get an error if I search for documentation as suggested in this tutorial:

% search_doc("numerical approximation")
  Warning: the Sage documentation is not available

Otherwise, it appears the Sage system is OK - but I am a complete beginner.

Environment

My platform:

 %  lsb_release -a 
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 18.04.4 LTS
Release:	18.04
Codename:	bionic

output of conda list:

% conda list

conda_list.zip

 % conda info                

     active environment : SageMath
    active env location : /home/______/miniconda3/envs/SageMath
            shell level : 2
       user config file : /home/______/.condarc
 populated config files : /home/______/.condarc
          conda version : 4.8.3
    conda-build version : not installed
         python version : 3.7.6.final.0
       virtual packages : __cuda=10.1
                          __glibc=2.27
       base environment : /home/______/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          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
          package cache : /home/______/miniconda3/pkgs
                          /home/______/.conda/pkgs
       envs directories : /home/______/miniconda3/envs
                          /home/______/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.6 Linux/5.3.0-53-generic ubuntu/18.04.4 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False