Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

libgit issues with Julia 1.6.5 h989b2f6_0 #166

Closed
mkitti opened this issue Jan 3, 2022 · 13 comments
Closed

libgit issues with Julia 1.6.5 h989b2f6_0 #166

mkitti opened this issue Jan 3, 2022 · 13 comments

Comments

@mkitti
Copy link
Contributor

mkitti commented Jan 3, 2022

There seem to be potential libgit2 issues with Julia 1.6.5 h989b2f6_0

$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.5 (2021-12-19)
 _/ |\__'_|_|_|\__'_|  |  conda-forge-julia release
|__/                   |

(@julia171_test) pkg> activate --temp
  Activating new environment at `/tmp/jl_wZ4SZa/Project.toml`

(jl_wZ4SZa) pkg> add https://github.com/mkitti/libcxxwrap_julia_jll_mock.git#cf
    Updating git-repo `https://github.com/mkitti/libcxxwrap_julia_jll_mock.git`
ERROR: failed to fetch from https://github.com/mkitti/libcxxwrap_julia_jll_mock.git, error: GitError(Code:ERROR, Class:Invalid, invalid version 0 on git_proxy_options)

(jl_wZ4SZa) pkg> add https://github.com/mkitti/libcxxwrap_julia_jll_mock.git
    Updating git-repo `https://github.com/mkitti/libcxxwrap_julia_jll_mock.git`
ERROR: failed to fetch from https://github.com/mkitti/libcxxwrap_julia_jll_mock.git, error: GitError(Code:ERROR, Class:Invalid, invalid version 0 on git_proxy_options)


$ conda list
# packages in environment at /home/mkitti/anaconda3/envs/julia171_test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
curl                      7.80.0               h494985f_1    conda-forge
expat                     2.4.2                h9c3ff4c_0    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
git                       2.34.1          pl5321hf874766_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
julia                     1.6.5                h989b2f6_0    conda-forge
krb5                      1.19.2               h48eae69_3    conda-forge
libblas                   3.9.0           12_linux64_openblas    conda-forge
libcblas                  3.9.0           12_linux64_openblas    conda-forge
libcurl                   7.80.0               h494985f_1    conda-forge
libcxxwrap-julia          0.8.3                h4bd325d_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                 11.2.0              h1d223b6_11    conda-forge
libgfortran-ng            11.2.0              h69a702a_11    conda-forge
libgfortran5              11.2.0              h5c6108e_11    conda-forge
libgit2                   1.3.0                haabb1ae_1    conda-forge
libgomp                   11.2.0              h1d223b6_11    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           12_linux64_openblas    conda-forge
libnghttp2                1.43.0               ha19adfc_1    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libopenblas-ilp64         0.3.18          pthreads_h0aa5bea_0    conda-forge
libssh2                   1.10.0               ha35d2d1_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libunwind                 1.5.0                h9c3ff4c_1    conda-forge
libutf8proc               2.7.0                h7f98852_0    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
mbedtls                   3.1.0                h9c3ff4c_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openblas-ilp64            0.3.18          pthreads_h3d04fff_0    conda-forge
openlibm                  0.7.0                h516909a_0    conda-forge
openssl                   3.0.0                h7f98852_2    conda-forge
p7zip                     16.02             he1b5a44_1000    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
perl                      5.32.1          1_h7f98852_perl5    conda-forge
suitesparse               5.10.1               h9e50725_1    conda-forge
tbb                       2021.5.0             h4bd325d_0    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
@mkitti
Copy link
Contributor Author

mkitti commented Jan 3, 2022

This seems to work fine:

$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.2 (2021-07-14)
 _/ |\__'_|_|_|\__'_|  |  conda-forge-julia release
|__/                   |

(@v1.6) pkg> activate --temp
  Activating new environment at `/tmp/jl_VdEGFV/Project.toml`

(jl_VdEGFV) pkg> add https://github.com/mkitti/libcxxwrap_julia_jll_mock.git#cf
    Updating git-repo `https://github.com/mkitti/libcxxwrap_julia_jll_mock.git`
    Updating registry at `~/.julia/registries/General`
   Resolving package versions...
    Updating `/tmp/jl_VdEGFV/Project.toml`
  [3eaa8342] + libcxxwrap_julia_jll v0.8.8+1 `https://github.com/mkitti/libcxxwrap_julia_jll_mock.git#cf`
    Updating `/tmp/jl_VdEGFV/Manifest.toml`
  [3eaa8342] + libcxxwrap_julia_jll v0.8.8+1 `https://github.com/mkitti/libcxxwrap_julia_jll_mock.git#cf`

$ conda list
# packages in environment at /home/mkitti/anaconda3/envs/julia162_test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.2               h7f98852_0    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
curl                      7.78.0               hea6ffbf_0    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
gettext                   0.19.8.1          h73d1719_1006    conda-forge
git                       2.33.0          pl5321hc30692c_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
julia                     1.6.2                h96f571d_0    conda-forge
krb5                      1.19.2               hcc1bbae_0    conda-forge
libblas                   3.9.0           11_linux64_openblas    conda-forge
libcblas                  3.9.0           11_linux64_openblas    conda-forge
libcurl                   7.78.0               h2574ce0_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h9c3ff4c_1    conda-forge
libgcc-ng                 11.1.0               hc902ee8_8    conda-forge
libgfortran-ng            11.1.0               h69a702a_8    conda-forge
libgfortran5              11.1.0               h6c583b3_8    conda-forge
libgit2                   1.1.1                hee63804_1    conda-forge
libgomp                   11.1.0               hc902ee8_8    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           11_linux64_openblas    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libopenblas-ilp64         0.3.17          pthreads_h0aa5bea_1    conda-forge
libssh2                   1.10.0               ha56f1ee_0    conda-forge
libstdcxx-ng              11.1.0               h56837e0_8    conda-forge
libunwind                 1.5.0                h9c3ff4c_1    conda-forge
libutf8proc               2.6.1                h7f98852_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openblas-ilp64            0.3.17          pthreads_h3d04fff_1    conda-forge
openlibm                  0.7.0                h516909a_0    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
p7zip                     16.02             he1b5a44_1000    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
perl                      5.32.1          0_h7f98852_perl5    conda-forge
suitesparse               5.4.0                h717dc36_0    conda-forge
tbb                       2020.2               h4bd325d_4    conda-forge
tk                        8.6.11               h27826a3_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge

@mkitti
Copy link
Contributor Author

mkitti commented Jan 3, 2022

I see. 1.6 branch probably needs 233c339

Fix in #159 ?

@ngam
Copy link
Contributor

ngam commented Jan 3, 2022

Ugh... I thought the libgit patch wasn't needed for the 1.6.x versions... We may want to actually solve this more properly later; I think we could work on constraining the exact version they're relying on upstream. I remember looking into it (you either apply the patch) or constrain libgit like libunwind, etc.

@mkitti
Copy link
Contributor Author

mkitti commented Jan 3, 2022

Upstream is pinned at libgit2 version 1.1.0.
https://github.com/JuliaLang/julia/blob/v1.6.5/deps/libgit2.version

@mkitti
Copy link
Contributor Author

mkitti commented Jan 3, 2022

See also

JuliaLang/julia#42209 (libgit2 version 1.2)
JuliaLang/julia#43250 (libgit2 version 1.3)

@ngam

This comment has been minimized.

Sign in to view
@ngam
Copy link
Contributor

ngam commented Jan 3, 2022

nvm sorry, it should take care of it, I think

@mkitti
Copy link
Contributor Author

mkitti commented Jan 3, 2022

1.7.1 is pinned at the same version, and the patch does seem to work.

@ngam
Copy link
Contributor

ngam commented Jan 3, 2022

1.7.1 is pinned at the same version, and the patch does seem to work.

Yep, sorry I wrote that without thinking! Will hide the comment :)

@ngam ngam mentioned this issue Jan 5, 2022
Merged
5 tasks
@ngam ngam closed this as completed Jan 6, 2022
@MilesCranmer
Copy link

Sorry to ping this old thread - I expanded the PySR unit tests to include conda-forge on macOS, and am seeing this issue here: https://github.com/MilesCranmer/PySR/actions/runs/3060750059/jobs/4939640457#step:5:155. Any idea why this is occuring?

@mkitti
Copy link
Contributor Author

mkitti commented Sep 15, 2022

The fix is to unset the environment variable JULIA_SSL_CA_ROOTS_PATH on macOS.

julia-feedstock/recipe/scripts/activate.sh

Lines 20 to 22 in a203b65

if [[ $OSTYPE != 'darwin'* ]]; then
export JULIA_SSL_CA_ROOTS_PATH=$CONDA_PREFIX/ssl/cacert.pem
fi

I think you need to unpin Julia from 1.7.1.

@MilesCranmer
Copy link

Awesome, thanks! Will unpin pysr now. Is it possible to backport it, just to generalize the solution to other versions?

@mkitti
Copy link
Contributor Author

mkitti commented Sep 16, 2022

The main issue is that Julia's mbedtls doesn't understand conda-forge's openssl certificate format.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@MilesCranmer @mkitti @ngam