conda-forge / julia-feedstock

A conda-smithy repository for julia.

About julia-feedstock

Feedstock license: BSD-3-Clause

Home: http://julialang.org/

Package license: MIT

Summary: A high-performance dynamic programming language for data science

Development: https://github.com/JuliaLang/julia

Documentation: https://docs.julialang.org

Julia is a high-level, high-performance dynamic language for technical computing. The main homepage for Julia can be found at julialang.org.

Current build status

Azure

Variant Status linux_64 osx_64

Current release info

Name	Downloads	Version	Platforms

Installing julia

Installing julia 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, julia can be installed with conda:

conda install julia

or with mamba:

mamba install julia

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

conda search julia --channel conda-forge

or with mamba:

mamba search julia --channel conda-forge

Alternatively, mamba repoquery may provide more information:

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

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

# List dependencies of `julia`:
mamba repoquery depends julia --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 julia-feedstock

If you would like to improve the julia 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/julia-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

• @SylvainCorlay
• @abhi18av
• @acaprez
• @bgruening
• @dfornika
• @mariusvniekerk
• @mkitti
• @ngam

julia-feedstock's Issues

Conda Installs old version of Julia 1.0.0 instead of Julia 1.0.2

Hello,

When I install the Julia package with conda (instructions in the site below), conda installs Julia 1.0.0, even though it says 1.0.2 on the package website. See below.

https://anaconda.org/conda-forge/julia

There are some important fixes in the new version, can you update the package to the current version? Can you make it so that I can use conda update julia so that it updates to the current version? Otherwise, I am going to have remove the current install and that has cause issues in the past where I have to remove the entire miniconda installation.

Thanks,

Alfredo

Failling to install Julia

Hi! Thanks for maintaining this package! I've an issue when I try to install it. I've got the following error message.

I have no idea how to solve this problem...

Issue:

ERROR conda.core.link:_execute(700): An error occurred while installing package 'conda-forge::julia-1.0.3-blas_openblash12d65f3_2'.
Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::julia-1.0.3-blas_openblash12d65f3_2
location of failed script: /home1/datahome/cviolet/.conda/envs/Hmsc/bin/.julia-post-link.sh
==> script messages <==
ERROR: failed to clone from https://github.com/JuliaRegistries/General.git, error: GitError(Code:ERROR, Class:Invalid, invalid version 0 on git_proxy_options)
Stacktrace:
 [1] pkgerror(::String) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:120
 [2] #clone#2(::String, ::Base.Iterators.Pairs{Symbol,LibGit2.CachedCredentials,Tuple{Symbol},NamedTuple{(:credentials,),Tuple{LibGit2.CachedCredentials}}}, ::Function, ::String, ::String) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/GitTools.jl:107
 [3] #clone at ./none:0 [inlined]
 [4] (::getfield(Pkg.Types, Symbol("##51#55")))(::LibGit2.CachedCredentials) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:937
 [5] shred!(::getfield(Pkg.Types, Symbol("##51#55")), ::LibGit2.CachedCredentials) at ./secretbuffer.jl:184
 [6] #registries#50(::Bool, ::Function) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:933
 [7] registries at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:917 [inlined]
 [8] #find_registered!#59(::Bool, ::Function, ::Pkg.Types.EnvCache, ::Array{String,1}, ::Array{Base.UUID,1}) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:999
 [9] #find_registered! at ./none:0 [inlined]
 [10] #find_registered!#65 at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:1017 [inlined]
 [11] find_registered! at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Types.jl:1017 [inlined]
 [12] deps_graph(::Pkg.Types.Context, ::Dict{Base.UUID,String}, ::Dict{Base.UUID,Pkg.Types.VersionSpec}, ::Dict{Base.UUID,Pkg.Types.Fixed}) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:294
 [13] resolve_versions!(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}, ::Nothing) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:371
 [14] resolve_versions! at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:316 [inlined]
 [15] up(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1244
 [16] #up#29(::Pkg.Types.UpgradeLevel, ::Pkg.Types.PackageMode, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:198
 [17] up at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:171 [inlined]
 [18] #up#24 at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:163 [inlined]
 [19] up at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:163 [inlined]
 [20] #instantiate#59(::Nothing, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context) at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:534
 [21] #instantiate#58 at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:532 [inlined]
 [22] instantiate() at /home/conda/feedstock_root/build_artifacts/julia_1548684429855/work/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:530
 [23] top-level scope at none:0
 Resolving package versions...
   Cloning default registries into /home1/datahome/cviolet/.julia/registries
   Cloning registry General from "https://github.com/JuliaRegistries/General.git"

==> script output <==
stdout: 
stderr: 
return code: 1

()

Environment (conda list):

$ conda list
# packages in environment at /home1/datahome/cviolet/.conda/envs/Hmsc:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_r-mutex                  1.0.0               anacondar_1  
attrs                     19.3.0                     py_0  
backcall                  0.1.0                    py37_0  
binutils_impl_linux-64    2.33.1               he6710b0_7  
binutils_linux-64         2.33.1              h9595d00_15  
bleach                    3.1.0                    py37_0  
bwidget                   1.9.11                        1  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2019.11.28           hecc5488_0    conda-forge
cairo                     1.14.12              h8948797_3  
certifi                   2019.11.28               py37_0    conda-forge
curl                      7.67.0               hbc83047_0  
decorator                 4.4.1                      py_0  
defusedxml                0.6.0                      py_0  
entrypoints               0.3                      py37_0  
fontconfig                2.13.0               h9420a91_0  
freetype                  2.9.1                h8a8886c_1  
fribidi                   1.0.5                h7b6447c_0  
gcc_impl_linux-64         7.3.0                habb00fd_1  
gcc_linux-64              7.3.0               h553295d_15  
gfortran_impl_linux-64    7.3.0                hdf63c60_1  
gfortran_linux-64         7.3.0               h553295d_15  
glib                      2.63.1               h5a9c865_0  
gmp                       6.1.2                h6c8ec71_1  
graphite2                 1.3.13               h23475e2_0  
gsl                       2.4               h294904e_1006    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1  
gxx_linux-64              7.3.0               h553295d_15  
harfbuzz                  1.8.8                hffaf4a1_0  
icu                       58.2                 h9c2bf20_1  
importlib_metadata        1.5.0                    py37_0  
ipykernel                 5.1.4            py37h39e3cac_0  
ipython                   7.12.0           py37h5ca1d4c_0  
ipython_genutils          0.2.0                    py37_0  
jags                      4.3.0             hc6cf775_1003    conda-forge
jedi                      0.16.0                   py37_0  
jinja2                    2.11.1                     py_0  
jpeg                      9b                   h024ee3a_2  
jsonschema                3.2.0                    py37_0  
jupyter_client            5.3.4                    py37_0  
jupyter_core              4.6.1                    py37_0  
krb5                      1.16.4               h173b8e3_0  
ld_impl_linux-64          2.33.1               h53a641e_7  
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libcurl                   7.67.0               h20c2e04_0  
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
liblapack                 3.8.0               14_openblas    conda-forge
libopenblas               0.3.7                h5ec1e0e_6    conda-forge
libpng                    1.6.37               hbc83047_0  
libsodium                 1.0.16               h1bed415_0  
libssh2                   1.8.2                h1ba5d50_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
libtiff                   4.1.0                h2733197_0  
libuuid                   1.0.3                h1bed415_2  
libxcb                    1.13                 h1bed415_1  
libxml2                   2.9.9                hea5a465_1  
make                      4.2.1                h1bed415_1  
markupsafe                1.1.1            py37h7b6447c_0  
mistune                   0.8.4            py37h7b6447c_0  
nbconvert                 5.6.1                    py37_0  
nbformat                  5.0.4                      py_0  
ncurses                   6.1                  he6710b0_1  
notebook                  6.0.3                    py37_0  
openssl                   1.1.1d               h516909a_0    conda-forge
pandoc                    2.2.3.2                       0  
pandocfilters             1.4.2                    py37_1  
pango                     1.42.4               h049681c_0  
parso                     0.6.1                      py_0  
pcre                      8.43                 he6710b0_0  
pexpect                   4.8.0                    py37_0  
pickleshare               0.7.5                    py37_0  
pip                       20.0.2                   py37_1  
pixman                    0.38.0               h7b6447c_0  
prometheus_client         0.7.1                      py_0  
prompt_toolkit            3.0.3                      py_0  
ptyprocess                0.6.0                    py37_0  
pygments                  2.5.2                      py_0  
pyrsistent                0.15.7           py37h7b6447c_0  
python                    3.7.6                h0371630_2  
python-dateutil           2.8.1                      py_0  
pyzmq                     17.1.2           py37h14c3975_0  
r-abind                   1.4_5           r36h6115d3f_1002    conda-forge
r-askpass                 1.0               r36h14c3975_0  
r-assertthat              0.2.1             r36h6115d3f_0  
r-backports               1.1.4             r36h96ca727_0  
r-base                    3.6.1                h9bb98a2_1  
r-base64enc               0.1_3             r36h96ca727_4  
r-bh                      1.69.0_1          r36h6115d3f_0  
r-boot                    1.3_20            r36h6115d3f_0  
r-broom                   0.5.2             r36h6115d3f_0  
r-callr                   3.2.0             r36h6115d3f_0  
r-caret                   6.0_83            r36h96ca727_0  
r-cellranger              1.1.0             r36h6115d3f_0  
r-class                   7.3_15            r36h96ca727_0  
r-cli                     1.1.0             r36h6115d3f_0  
r-clipr                   0.6.0             r36h6115d3f_0  
r-cluster                 2.0.8             r36ha65eedd_0  
r-coda                    0.19_3            r36h6115d3f_1    conda-forge
r-codetools               0.2_16            r36h6115d3f_0  
r-colorspace              1.4_1             r36h96ca727_0  
r-crayon                  1.3.4             r36h6115d3f_0  
r-curl                    3.3               r36h96ca727_0  
r-data.table              1.12.2            r36h96ca727_0  
r-dbi                     1.0.0             r36h6115d3f_0  
r-dbplyr                  1.4.0             r36h6115d3f_0  
r-dichromat               2.0_0             r36h6115d3f_4  
r-digest                  0.6.18            r36h96ca727_0  
r-dplyr                   0.8.0.1           r36h29659fb_0  
r-ellipsis                0.1.0             r36h96ca727_0  
r-essentials              3.6.0                     r36_0  
r-evaluate                0.13              r36h6115d3f_0  
r-fansi                   0.4.0             r36h96ca727_0  
r-forcats                 0.4.0             r36h6115d3f_0  
r-foreach                 1.4.4             r36h6115d3f_0  
r-foreign                 0.8_71            r36h96ca727_0  
r-formatr                 1.6               r36h6115d3f_0  
r-fs                      1.2.7             r36h29659fb_0  
r-generics                0.0.2             r36h6115d3f_0  
r-ggplot2                 3.1.1             r36h6115d3f_0  
r-glmnet                  2.0_16            r36ha65eedd_0  
r-glue                    1.3.1             r36h96ca727_0  
r-gower                   0.2.0             r36h96ca727_0  
r-gtable                  0.3.0             r36h6115d3f_0  
r-haven                   2.1.0             r36h29659fb_0  
r-hexbin                  1.27.2            r36ha65eedd_0  
r-highr                   0.8               r36h6115d3f_0  
r-hms                     0.4.2             r36h6115d3f_0  
r-htmltools               0.3.6             r36h29659fb_0  
r-htmlwidgets             1.3               r36h6115d3f_0  
r-httpuv                  1.5.1             r36h29659fb_0  
r-httr                    1.4.0             r36h6115d3f_0  
r-ipred                   0.9_8             r36h96ca727_0  
r-irdisplay               0.7.0             r36h6115d3f_0  
r-irkernel                0.8.15                    r36_0  
r-iterators               1.0.10            r36h6115d3f_0  
r-jsonlite                1.6               r36h96ca727_0  
r-kernsmooth              2.23_15           r36ha65eedd_4  
r-knitr                   1.22              r36h6115d3f_0  
r-labeling                0.3               r36h6115d3f_4  
r-later                   0.8.0             r36h29659fb_0  
r-lattice                 0.20_38           r36h96ca727_0  
r-lava                    1.6.5             r36h6115d3f_0  
r-lazyeval                0.2.2             r36h96ca727_0  
r-lubridate               1.7.4             r36h29659fb_0  
r-magrittr                1.5               r36h6115d3f_4  
r-maps                    3.3.0             r36h96ca727_0  
r-markdown                0.9               r36h96ca727_0  
r-mass                    7.3_51.3          r36h96ca727_0  
r-matrix                  1.2_17            r36h96ca727_0  
r-mgcv                    1.8_28            r36h96ca727_0  
r-mime                    0.6               r36h96ca727_0  
r-modelmetrics            1.2.2             r36h29659fb_0  
r-modelr                  0.1.4             r36h6115d3f_0  
r-munsell                 0.5.0             r36h6115d3f_0  
r-nlme                    3.1_139           r36ha65eedd_0  
r-nnet                    7.3_12            r36h96ca727_0  
r-numderiv                2016.8_1          r36h6115d3f_0  
r-openssl                 1.3               r36h96ca727_0  
r-pbdzmq                  0.3_3             r36h29659fb_0  
r-pillar                  1.3.1             r36h6115d3f_0  
r-pkgconfig               2.0.2             r36h6115d3f_0  
r-plogr                   0.2.0             r36h6115d3f_0  
r-plyr                    1.8.4             r36h29659fb_0  
r-prettyunits             1.0.2             r36h6115d3f_0  
r-processx                3.3.0             r36h96ca727_0  
r-prodlim                 2018.04.18        r36h29659fb_0  
r-progress                1.2.0             r36h6115d3f_0  
r-promises                1.0.1             r36h29659fb_0  
r-ps                      1.3.0             r36h96ca727_0  
r-purrr                   0.3.2             r36h96ca727_0  
r-quantmod                0.4_14            r36h6115d3f_0  
r-r2jags                  0.5_7             r36h6115d3f_1    conda-forge
r-r2winbugs               2.1_21            r36h6115d3f_1    conda-forge
r-r6                      2.4.0             r36h6115d3f_0  
r-randomforest            4.6_14            r36ha65eedd_0  
r-rbokeh                  0.6.3                     r36_0  
r-rcolorbrewer            1.1_2             r36h6115d3f_0  
r-rcpp                    1.0.1             r36h29659fb_0  
r-rcpproll                0.3.0             r36h29659fb_0  
r-readr                   1.3.1             r36h29659fb_0  
r-readxl                  1.3.1             r36h29659fb_0  
r-recipes                 0.1.5             r36h6115d3f_0  
r-recommended             3.6.0                     r36_0  
r-rematch                 1.0.1             r36h6115d3f_0  
r-repr                    0.19.2            r36h6115d3f_0  
r-reprex                  0.2.1             r36h6115d3f_0  
r-reshape2                1.4.3             r36h29659fb_0  
r-rjags                   4_10              r36h0357c0b_0    conda-forge
r-rlang                   0.3.4             r36h96ca727_0  
r-rmarkdown               1.12              r36h6115d3f_0  
r-rpart                   4.1_15            r36h96ca727_0  
r-rstudioapi              0.10              r36h6115d3f_0  
r-rvest                   0.3.3             r36h6115d3f_0  
r-scales                  1.0.0             r36h29659fb_0  
r-selectr                 0.4_1             r36h6115d3f_0  
r-shiny                   1.3.2             r36h6115d3f_0  
r-sourcetools             0.1.7             r36h29659fb_0  
r-spatial                 7.3_11            r36h96ca727_4  
r-squarem                 2017.10_1         r36h6115d3f_0  
r-stringi                 1.4.3             r36h29659fb_0  
r-stringr                 1.4.0             r36h6115d3f_0  
r-survival                2.44_1.1          r36h96ca727_0  
r-sys                     3.2               r36h96ca727_0  
r-tibble                  2.1.1             r36h96ca727_0  
r-tidyr                   0.8.3             r36h29659fb_0  
r-tidyselect              0.2.5             r36h29659fb_0  
r-tidyverse               1.2.1             r36h6115d3f_0  
r-timedate                3043.102          r36h6115d3f_0  
r-tinytex                 0.12              r36h6115d3f_0  
r-ttr                     0.23_4            r36ha65eedd_0  
r-utf8                    1.1.4             r36h96ca727_0  
r-uuid                    0.1_2             r36h96ca727_4  
r-viridislite             0.3.0             r36h6115d3f_0  
r-whisker                 0.3_2             r36h6115d3f_4  
r-withr                   2.1.2             r36h6115d3f_0  
r-xfun                    0.6               r36h6115d3f_0  
r-xml2                    1.2.0             r36h29659fb_0  
r-xtable                  1.8_4             r36h6115d3f_0  
r-xts                     0.11_2            r36h96ca727_0  
r-yaml                    2.2.0             r36h96ca727_0  
r-zoo                     1.8_6             r36h96ca727_0  
readline                  7.0                  h7b6447c_5  
send2trash                1.5.0                    py37_0  
setuptools                45.2.0                   py37_0  
six                       1.14.0                   py37_0  
sqlite                    3.31.1               h7b6447c_0  
terminado                 0.8.3                    py37_0  
testpath                  0.4.4                      py_0  
tk                        8.6.8                hbc83047_0  
tktable                   2.10                 h14c3975_0  
tornado                   6.0.3            py37h7b6447c_3  
traitlets                 4.3.3                    py37_0  
wcwidth                   0.1.8                      py_0  
webencodings              0.5.1                    py37_1  
wheel                     0.34.2                   py37_0  
xz                        5.2.4                h14c3975_4  
zeromq                    4.2.5                hf484d3e_1  
zipp                      2.2.0                      py_0  
zlib                      1.2.11               h7b6447c_3  
zstd                      1.3.7                h0b5b093_0  

Details about conda and system ( conda info ):

$ conda info
     active environment : Hmsc
    active env location : /home1/datahome/cviolet/.conda/envs/Hmsc
            shell level : 1
       user config file : /home1/datahome/cviolet/.condarc
 populated config files : /home1/datahome/cviolet/.condarc
          conda version : 4.8.2
    conda-build version : 3.18.9
         python version : 3.7.4.final.0
       virtual packages : __glibc=2.19
       base environment : /appli/anaconda/versions/4.8.2  (read only)
           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 : /appli/anaconda/versions/4.8.2/pkgs
                          /home1/datahome/cviolet/.conda/pkgs
       envs directories : /home1/datahome/cviolet/.conda/envs
                          /appli/anaconda/versions/4.8.2/envs
               platform : linux-64
             user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.4 Linux/3.12.53-60.30-default sles/12.1 glibc/2.19
                UID:GID : 502852:10571
             netrc file : None
           offline mode : False

Remove wrapper script

Raising in part due to this request.

Would be good if the wrappers script could be replaced with a juliarc file instead. This would allow us to use a stock solution to this problem. In turn this would make it easier to get to the bottom of bugs we encounter when discussing with upstream.

Incompatibility between latest `julia=1.7.1` and latest `openlibm=0.8.0` on `conda-forge`

Hey guys, Happy New Year! Just a heads up that the latest Julia can not be installed in a conda env with deps from conda-forge unless one pins openlibm=0.7.0 (presumably a pin like openlibm<0.8 should work too) since the latest openlibm is now 0.8.0 as of 12 hours ago; see our issue on this matter ESMValGroup/ESMValTool#2450 Cheers 🍺

Julia packages

Opening this issue to discuss how to best handle Julia packages with conda.

Supporting newer versions

Thanks for everyone's work towards making Julia available via conda! It looks like there are some changes to the Julia build system post 1.1 that are preventing this conda build from succeeding (see #74, #78. and #80). I just wanted to check if there looks to be a quick fix to anyone more experienced with building Julia than myself, before I dig into the details.

Require libuv

One of Julia's requirements is libuv, which we already have packaged at conda-forge. Would be good to make use of our libuv instead of allowing it to build its own.

Julia conda-forge package gives segmentation fault

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

Issue: After installing Julia in a conda environment under Ubuntu with conda-forge and trying to add a Julia package, you get a segmentation fault. If you install Julia (same version) in the standard way for Ubuntu, it works correctly. Reproduced with multiple Ubuntu versions.

Environment (conda list):

$ conda list
# packages in environment at /root/anaconda3/envs/julia-test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main
_openmp_mutex             4.5                       1_gnu
ca-certificates           2021.10.26           h06a4308_2
libgcc-ng                 9.3.0               h5101ec6_17
libgomp                   9.3.0               h5101ec6_17
openssl                   1.1.1l               h7f8727e_0

Details about conda and system ( conda info ):

$ conda info
     active environment : julia-test
    active env location : /root/anaconda3/envs/julia-test
            shell level : 2
       user config file : /root/.condarc
 populated config files :
          conda version : 4.10.3
    conda-build version : 3.21.5
         python version : 3.9.7.final.0
       virtual packages : __linux=5.10.16.3=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /root/anaconda3  (writable)
      conda av data dir : /root/anaconda3/etc/conda
  conda av metadata url : None
           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 : /root/anaconda3/pkgs
                          /root/.conda/pkgs
       envs directories : /root/anaconda3/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.7 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/18.04.6 glibc/2.27
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Reproduction steps:

# Run an Ubuntu container
docker run -it ubuntu:18.04
# Set up image
apt-get update
apt-get install wget
# Install anaconda
wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh
bash Anaconda3-2021.11-Linux-x86_64.sh
# Create a new shell and conda environment
bash
conda create --name julia-test
conda activate julia-test
# Install julia
conda install -c conda-forge julia
# Try adding a package
julia -e 'import Pkg; Pkg.add("Calculus");'

Result is:

(julia-test) root@b15ea6be3ef7:/# julia --version
julia version 1.6.4
(julia-test) root@b15ea6be3ef7:/# julia -e 'import Pkg; Pkg.add("Calculus");'
  Installing known registries into `~/.julia`
Segmentation fault                                        ]  0.0 %

updates + plan

@mkitti

How about the following plan going forward in order:

1. we need to fix the prelink, etc. problems and investigates more of the issues
2. we need a separate LTS branch (for 1.6 and its updates)
3. we need to fix the patches, etc. for julia 1.7, and then build for arm and so on (these are ready, but let's not merge yet)

For now keep the 1.7 and libunwind 1.6 PRs open with no action, and let's focus on immediately fixing any problems. Then we open an LTS branch. Then we focus on v1.7.

What's the latest regarding fixing the linking problems and/or any other issues?

• 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

SuiteSparse Compatiblility with Sundials.jl

On the new v1.6.1 installing and precompiling Sundials.jl (dependency of DifferentialEquations.jl) gives:

ERROR: LoadError: InitError: could not load library "/Users/mattjohnson/.julia/artifacts/bd8ae81b8657ac029ad0b2592aaba09a79121a96/lib/libsundials_sunlinsolklu.3.2.0.dylib"
dlopen(/Users/mattjohnson/.julia/artifacts/bd8ae81b8657ac029ad0b2592aaba09a79121a96/lib/libsundials_sunlinsolklu.3.2.0.dylib, 1): Library not loaded: @rpath/libsuitesparseconfig.5.4.0.dylib
Referenced from: /Users/mattjohnson/.julia/artifacts/bd8ae81b8657ac029ad0b2592aaba09a79121a96/lib/libsundials_sunlinsolklu.3.2.0.dylib
Reason: image not found

This seems to be due to the suitesparse version choice: SciML/Sundials.jl#303. Building instead with suitesparse 5.4.0 fixes this issue. This might not be an issue after Julia 1.7 in BinaryBuillder it looks like they're planning to move to 5.10.0 for Julia 1.7.

Julia has latest version 1.6.1, but through conda forde I am only able to acheive julia 1.1.1. How to upgrade to latest version?

• 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

Failling to install Julia v1.1.1

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

Issue:
Problem: package julia-1.1.1-h14ade15_2 requires libgit2 >=0.27.8,<0.28.0a0, but none of the providers can be installed

~|___(0.0) mamba install julia=1.1.1

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

mamba (0.7.3) supported by @QuantStack

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

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


Looking for: ['julia=1.1.1']

conda-forge/linux-64     [====================] (00m:00s) No change
conda-forge/noarch       [====================] (00m:00s) No change
bioconda/noarch          [====================] (00m:00s) No change
biobakery/linux-64       [====================] (00m:00s) No change
anaconda/pkgs/main/linux [====================] (00m:00s) No change
ohmeta/noarch            [====================] (00m:00s) No change
ursky/linux-64           [====================] (00m:00s) No change
ursky/noarch             [====================] (00m:00s) No change
bioconda/linux-64        [====================] (00m:00s) No change
biobakery/noarch         [====================] (00m:00s) No change
anaconda/pkgs/main/noarc [====================] (00m:00s) No change
anaconda/pkgs/free/linux [====================] (00m:00s) No change
anaconda/pkgs/free/noarc [====================] (00m:00s) No change
qiime2/noarch            [====================] (00m:00s) No change
anaconda/pkgs/r/linux-64 [====================] (00m:00s) No change
anaconda/pkgs/r/noarch   [====================] (00m:00s) No change
qiime2/linux-64          [====================] (00m:00s) No change
ohmeta/linux-64          [====================] (00m:00s) No change
Encountered problems while solving.
Problem: package julia-1.1.1-h14ade15_2 requires libgit2 >=0.27.8,<0.28.0a0, but none of the providers can be installed

Environment (conda list):

$ conda info
~|___(0.0) conda info

active environment : None
shell level : 0
user config file : /home/zhujie/.condarc
populated config files : /home/zhujie/.condarc
conda version : 4.9.2
conda-build version : 3.20.5
python version : 3.7.8.final.0
virtual packages : __glibc=2.17=0
__unix=0=0
__archspec=1=x86_64
base environment : /ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.7  (writable)
channel URLs : https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/linux-64
https://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/noarch
https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/linux-64
https://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/noarch
https://mirrors.bfsu.edu.cn/anaconda/cloud/biobakery/linux-64
https://mirrors.bfsu.edu.cn/anaconda/cloud/biobakery/noarch
https://mirrors.bfsu.edu.cn/anaconda/cloud/qiime2/linux-64
https://mirrors.bfsu.edu.cn/anaconda/cloud/qiime2/noarch
https://mirrors.bfsu.edu.cn/anaconda/cloud/ohmeta/linux-64
https://mirrors.bfsu.edu.cn/anaconda/cloud/ohmeta/noarch
https://mirrors.bfsu.edu.cn/anaconda/cloud/ursky/linux-64
https://mirrors.bfsu.edu.cn/anaconda/cloud/ursky/noarch
https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/linux-64
https://mirrors.bfsu.edu.cn/anaconda/pkgs/main/noarch
https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/linux-64
https://mirrors.bfsu.edu.cn/anaconda/pkgs/free/noarch
https://mirrors.bfsu.edu.cn/anaconda/pkgs/r/linux-64
https://mirrors.bfsu.edu.cn/anaconda/pkgs/r/noarch
package cache : /ldfssz1/ST_META/share/User/zhujie/.conda/pkgs
envs directories : /ldfssz1/ST_META/share/User/zhujie/.conda/envs
/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.7/envs
/home/zhujie/.conda/envs
platform : linux-64
user-agent : conda/4.9.2 requests/2.25.0 CPython/3.7.8 Linux/3.10.0-862.el7.x86_64 centos/7.5.1804 glibc/2.17
UID:GID : 666715:2782
netrc file : None
offline mode : False

OS X build

Is there a major obstacle for an OS X build? (I guess a windows build would be more difficult and require msys2 dependencies.)

julia: enable all tests + stricter pinning

This is an issue to track progress and discussion regarding the two points below.

• We ought to conduct all tests available upstream (unless they run over 6 hours).

• Based on the issues we faced with libunwind and now openlibm, we should consider more exact pinning going forward.

---

• 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

increase number of cores for testing

julia-feedstock/recipe/meta.yaml

Lines 70 to 80 in 1cbc3c9

	test:
	commands:
	- julia -e 'Base.runtests(["subarray", "core", "compiler", "worlds", "keywordargs", "numbers", "subtype", "char", "strings", "triplequote", "unicode", "intrinsics", "dict", "hashing", "iobuffer", "staged", "offsetarray", "arrayops", "tuple", "reduce", "reducedim", "abstractarray", "intfuncs", "simdloop", "vecelement",
	"rational", "bitarray", "copy", "fastmath", "functional", "iterators", "operators", "ordering", "path", "ccall", "parse", "loading", "gmp", "sorting", "spawn", "backtrace", "exceptions", "file", "read", "version", "namedtuple", "mpfr", "broadcast", "complex", "floatapprox", "reflection", "regex", "float16", "combinatorics",
	"sysinfo", "env", "rounding", "ranges", "mod2pi", "euler", "show", "client", "errorshow", "sets", "goto", "llvmcall", "llvmcall2", "ryu", "some", "meta", "stacktraces", "docs", "misc", "threads", "stress", "binaryplatforms", "atexit", "enums", "cmdlineargs", "int", "interpreter", "checked", "bitset", "floatfuncs",
	"precompile", "boundscheck", "error", "ambiguous", "cartesian", "osutils", "channels", "iostream", "secretbuffer", "specificity", "reinterpretarray", "syntax", "corelogging", "missing", "asyncmap", "smallarrayshrink", "download"])' # all except stdlib, add "opaque_closure", "filesystem" with 1.7
	- julia -e 'Base.runtests(["math"])' # [not osx] due to failure on math.jl:296, pre-haswell processor
	- julia -e 'import Pkg;Pkg.add("LibSSH2_jll")'
	- julia -e 'import Pkg;Pkg.add("Sundials")'
	requires:
	- perl

What's the command for using all available cores/threads? I noticed that julia -e "..." would use number of threads - 1 (so 8 threads yield 7 workers, etc.)

@mkitti any ideas?

---

• 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

bitarray test slow

Frequently the bitarray test takes too long to complete on the CIs. A sample build log is linked below. Is there something we can do to fix this? Should we just skip it?

ref: https://circleci.com/gh/conda-forge/julia-feedstock/62

Cannot conda install julia=1.6.3 after succesfully installing julia=1.6.4

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

Issue:
I cannot install julia=1.6.3 after isntalling 1.6.4. There is a warning issued "Consider notifying the package maintainer"

Reproduce in a fresh env:

conda create -n juliaenv python=3.8
conda activate juliaenv 
conda install -c conda-forge julia=1.6.4   # this works 
conda install -c conda-forge julia=1.6.3  # this fails

Stacktrace:

(juliaenv) ➜  lasso git:(julia) ✗ conda install -c conda-forge julia=1.6.3
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: done

## Package Plan ##

  environment location: /home/mathurin/anaconda3/envs/juliaenv

  added / updated specs:
    - julia=1.6.3


The following packages will be DOWNGRADED:

  julia                                    1.6.4-h2a39549_0 --> 1.6.3-h2a39549_1


Proceed ([y]/n)? 

Preparing transaction: done
Verifying transaction: done
Executing transaction: \ 
WARNING conda.core.link:run_script(1228): pre-unlink script failed for package conda-forge/linux-64::julia-1.6.4-h2a39549_0
consider notifying the package maintainer
| 
done
ERROR conda.core.link:_execute(699): An error occurred while installing package 'conda-forge::julia-1.6.3-h2a39549_1'.
Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::julia-1.6.3-h2a39549_1
location of failed script: /home/mathurin/anaconda3/envs/juliaenv/bin/.julia-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: 
stderr: /home/mathurin/anaconda3/envs/juliaenv/bin/.julia-post-link.sh: line 1: 139846 Segmentation fault      (core dumped) "${PREFIX}/bin/julia" -e 'using Pkg; Pkg.instantiate()' >> "${PREFIX}/.messages.txt" 2>&1

return code: 139

()

seems related to #132

Environment (conda list):

$ conda list
# packages in environment at /home/mathurin/anaconda3/envs/juliaenv:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    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
certifi                   2021.10.8        py38h578d9bd_1    conda-forge
curl                      7.80.0               h2574ce0_0    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
git                       2.34.1          pl5321hc30692c_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
julia                     1.6.4                h2a39549_0    conda-forge
krb5                      1.19.2               hcc1bbae_3    conda-forge
ld_impl_linux-64          2.35.1               h7274673_9  
libblas                   3.9.0           12_linux64_openblas    conda-forge
libcblas                  3.9.0           12_linux64_openblas    conda-forge
libcurl                   7.80.0               h2574ce0_0    conda-forge
libedit                   3.1.20210910         h7f8727e_0  
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  he6710b0_2  
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                hee63804_1    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           12_linux64_openblas    conda-forge
libnghttp2                1.43.0               h812cca2_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               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_11    conda-forge
libunwind                 1.6.0                h9c3ff4c_1    conda-forge
libutf8proc               2.6.1                h7f98852_0    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
llvm-openmp               12.0.1               h4bd325d_1    conda-forge
mbedtls                   3.0.0                h9c3ff4c_0    conda-forge
metis                     5.1.0             h58526e2_1006    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
ncurses                   6.3                  h7f8727e_2  
openblas-ilp64            0.3.18          pthreads_h3d04fff_0    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          1_h7f98852_perl5    conda-forge
pip                       21.2.4           py38h06a4308_0  
python                    3.8.12               h12debd9_0  
python_abi                3.8                      2_cp38    conda-forge
readline                  8.1                  h27cfd23_0  
setuptools                58.0.4           py38h06a4308_0  
sqlite                    3.36.0               hc218d9a_0  
suitesparse               5.10.1               h9e50725_1    conda-forge
tbb                       2021.4.0             h4bd325d_1    conda-forge
tk                        8.6.11               h1ccaba5_0  
wheel                     0.37.0             pyhd3eb1b0_1  
xz                        5.2.5                h7b6447c_0  
zlib                      1.2.11            h36c2ea0_1013    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : juliaenv
    active env location : /home/mathurin/anaconda3/envs/juliaenv
            shell level : 2
       user config file : /home/mathurin/.condarc
 populated config files : 
          conda version : 4.11.0
    conda-build version : 3.21.5
         python version : 3.9.7.final.0
       virtual packages : __linux=5.11.0=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/mathurin/anaconda3  (writable)
      conda av data dir : /home/mathurin/anaconda3/etc/conda
  conda av metadata url : None
           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/mathurin/anaconda3/pkgs
                          /home/mathurin/.conda/pkgs
       envs directories : /home/mathurin/anaconda3/envs
                          /home/mathurin/.conda/envs
               platform : linux-64
             user-agent : conda/4.11.0 requests/2.26.0 CPython/3.9.7 Linux/5.11.0-41-generic ubuntu/20.04.3 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

julia package missing on conda-forge

Issue:
I am fairly new to Anaconda and completely new to Julia, but tried to install this morning. I ran conda config --add channels conda-forge and can see that it has been successfully added when I run conda config --show-sources.

However, when I then try and install julia into my python27 environment, I get the following error:

$conda install -n python27 -c conda-forge julia
Fetching package metadata ...............

PackageNotFoundError: Packages missing in current channels:

• julia

We have searched for the packages in the following channels:

• https://conda.anaconda.org/conda-forge/win-64
• https://conda.anaconda.org/conda-forge/noarch
• https://repo.continuum.io/pkgs/main/win-64
• https://repo.continuum.io/pkgs/main/noarch
• https://repo.continuum.io/pkgs/free/win-64
• https://repo.continuum.io/pkgs/free/noarch
• https://repo.continuum.io/pkgs/r/win-64
• https://repo.continuum.io/pkgs/r/noarch
• https://repo.continuum.io/pkgs/pro/win-64
• https://repo.continuum.io/pkgs/pro/noarch
• https://repo.continuum.io/pkgs/msys2/win-64
• https://repo.continuum.io/pkgs/msys2/noarch

Environment (conda list -n python27):

$ conda list -n python27

# packages in environment at C:\Users\perryd\AppData\Local\conda\conda\envs\python27:
#
alabaster                 0.7.11                   py27_0  
appdirs                   1.4.3                    py27_0  
asn1crypto                0.24.0                   py27_0  
astroid                   1.6.5                    py27_0  
atom                      0.4.1            py27hc56fc5f_0    anaconda
attrs                     18.1.0                   py27_0  
automat                   0.7.0                    py27_0  
babel                     2.6.0                    py27_0  
backports                 1.0                      py27_1  
backports.functools_lru_cache 1.5                      py27_1  
backports.shutil_get_terminal_size 1.0.0                    py27_2  
backports.shutil_which    3.5.1                    py27_2  
backports_abc             0.5              py27h0ec6b72_0  
blas                      1.0                         mkl  
bleach                    2.1.3                    py27_0  
ca-certificates           2018.03.07                    0  
certifi                   2018.4.16                py27_0  
cffi                      1.11.5           py27hdb016f4_0  
chardet                   3.0.4                    py27_1  
cloudpickle               0.5.3                    py27_0  
colorama                  0.3.9            py27hdfe4ae1_0  
configparser              3.5.0            py27h2fa79a8_0  
constantly                15.1.0                   py27_0  
cryptography              2.2.2            py27h0c8e037_0  
cycler                    0.10.0                    <pip>
decorator                 4.3.0                    py27_0  
docutils                  0.14             py27h8652d09_0  
entrypoints               0.2.3                    py27_2  
enum34                    1.1.6                    py27_1  
functools32               3.2.3.2                  py27_1  
future                    0.16.0                   py27_1    anaconda
futures                   3.2.0                    py27_0  
html5lib                  1.0.1                    py27_0  
hyperlink                 18.0.0                   py27_0  
icc_rt                    2017.0.4             h97af966_0  
icu                       58.2                 h2aa20d9_1  
idna                      2.7                      py27_0  
imagesize                 1.0.0                    py27_0  
incremental               17.5.0           py27h502cdf3_0  
intel-openmp              2018.0.3                      0  
ipaddress                 1.0.22                   py27_0  
ipykernel                 4.8.2                    py27_0  
ipython                   5.8.0                    py27_0  
ipython_genutils          0.2.0            py27hbe997df_0  
isort                     4.3.4                    py27_0  
jedi                      0.12.1                   py27_0  
jinja2                    2.10                     py27_0  
jpeg                      9b                   ha175dff_2  
jsonschema                2.6.0            py27haaf3834_0  
jupyter_client            5.2.3                    py27_0  
jupyter_core              4.4.0                    py27_0  
keyring                   13.2.1                   py27_0  
kiwisolver                1.0.1                     <pip>
lazy-object-proxy         1.3.1            py27h0c8e037_2  
libpng                    1.6.34               h325896a_0  
libsodium                 1.0.16               h8b3e59e_0  
m2w64-gcc-libgfortran     5.3.0                         6  
m2w64-gcc-libs            5.3.0                         7  
m2w64-gcc-libs-core       5.3.0                         7  
m2w64-gmp                 6.1.0                         2  
m2w64-libwinpthread-git   5.0.0.4634.697f757               2  
markupsafe                1.0              py27h0c8e037_1  
matplotlib                2.2.2                     <pip>
mccabe                    0.6.1            py27hde0bf6e_1  
mistune                   0.8.3            py27h0c8e037_1  
mkl                       2018.0.3                      1  
mkl_fft                   1.0.4            py27h31cbb53_1  
msys2-conda-epoch         20160418                      1  
nbconvert                 5.3.1                    py27_0  
nbformat                  4.4.0            py27hf49b375_0  
notebook                  5.6.0                    py27_0  
numpy                     1.15.0           py27h911edcf_0  
numpy-base                1.15.0           py27hfef472a_0  
numpydoc                  0.8.0                    py27_0  
openssl                   1.0.2o               h2c51139_0  
packaging                 17.1                     py27_0  
pandoc                    2.2.1                h1a437c5_0  
pandocfilters             1.4.2                    py27_1  
parso                     0.3.1                    py27_0  
pathlib2                  2.3.2                    py27_0  
pickleshare               0.7.4            py27hb5f6335_0  
pip                       10.0.1                   py27_0  
prometheus_client         0.3.1                    py27_0  
prompt_toolkit            1.0.15           py27h3a8ec6a_0  
psutil                    5.4.6            py27h0c8e037_0  
pyasn1                    0.4.4                    py27_0  
pyasn1-modules            0.2.2                    py27_0  
pycodestyle               2.4.0                    py27_0  
pycparser                 2.18                     py27_1  
pyflakes                  2.0.0                    py27_0  
pygments                  2.2.0            py27ha50f84f_0  
pylint                    1.9.2                    py27_0  
pyopenssl                 18.0.0                   py27_0  
pyparsing                 2.2.0                    py27_1  
pyqt                      5.6.0            py27h224ed30_5  
pysocks                   1.6.8                    py27_0  
python                    2.7.15               he216670_0  
python-dateutil           2.7.3                    py27_0  
pytz                      2018.5                   py27_0  
pywin32                   223              py27h0c8e037_1  
pywinpty                  0.5.4                    py27_0  
pyzmq                     17.0.0           py27h0c8e037_3  
qt                        5.6.2            vc9hc26998b_12  [vc9]
qtawesome                 0.4.4            py27h766b13d_0  
qtconsole                 4.3.1            py27h77d40ac_0  
qtpy                      1.4.2                    py27_0  
requests                  2.19.1                   py27_0  
rope                      0.10.7           py27hb65afb6_0  
scandir                   1.7              py27h0c8e037_0  
scikit-learn              0.19.1           py27he00e316_0  
scipy                     1.1.0            py27ha6b90e7_0  
send2trash                1.5.0                    py27_0  
service_identity          17.0.0                   py27_0  
setuptools                39.2.0                   py27_0  
simplegeneric             0.8.1                    py27_2  
singledispatch            3.4.0.3          py27h3f9d112_0  
sip                       4.18.1           py27h5ec1c1a_2  
six                       1.11.0                   py27_1  
snowballstemmer           1.2.1            py27h28d3bf7_0  
sphinx                    1.7.6                    py27_0  
sphinxcontrib             1.0                      py27_1  
sphinxcontrib-websupport  1.1.0                    py27_1  
spyder                    3.3.0                    py27_0  
spyder-kernels            0.2.4                    py27_0  
sqlite                    3.24.0               h7a46e7a_0  
terminado                 0.8.1                    py27_1  
testpath                  0.3.1            py27h1cd488d_0  
tornado                   5.0.2            py27h0c8e037_0  
traitlets                 4.3.2            py27h1b1b3a5_0  
twisted                   18.4.0           py27h0c8e037_0  
typing                    3.6.4                    py27_0  
urllib3                   1.23                     py27_0  
vc                        9                    h7299396_1  
vs2008_runtime            9.00.30729.1         hfaea7d5_1  
wcwidth                   0.1.7            py27hb1a0d82_0  
webencodings              0.5.1                    py27_1  
wheel                     0.31.1                   py27_0  
win_inet_pton             1.0.1                    py27_1  
win_unicode_console       0.5              py27hc037021_0  
wincertstore              0.2              py27hf04cefb_0  
winpty                    0.4.3                         4  
wrapt                     1.10.11          py27h0c8e037_2  
zeromq                    4.2.5                h2880e7c_1  
zlib                      1.2.11               hbc2faf4_2  
zope                      1.0                      py27_0  
zope.interface            4.5.0            py27h0c8e037_0

Details about conda and system ( conda info ):

$ conda info
Current conda install:

               platform : win-64
          conda version : 4.3.30
       conda is private : False
      conda-env version : 4.3.30
    conda-build version : 3.0.27
         python version : 3.6.3.final.0
       requests version : 2.18.4
       root environment : C:\PROGRA~3\ANACON~1  (read only)
    default environment : C:\PROGRA~3\ANACON~1
       envs directories : C:\Users\perryd\AppData\Local\conda\conda\envs
                          C:\PROGRA~3\ANACON~1\envs
                          \\prd-file001.btn.opra.gov.uk\users$\perryd\Documents\.conda\envs
          package cache : C:\PROGRA~3\ANACON~1\pkgs
                          C:\Users\perryd\AppData\Local\conda\conda\pkgs
           channel URLs : https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.continuum.io/pkgs/main/win-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/win-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/win-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/win-64
                          https://repo.continuum.io/pkgs/pro/noarch
                          https://repo.continuum.io/pkgs/msys2/win-64
                          https://repo.continuum.io/pkgs/msys2/noarch
            config file : \\prd-file001.btn.opra.gov.uk\users$\perryd\Documents\.condarc
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.30 requests/2.18.4 CPython/3.6.3 Windows/10 Windows/10.0.14393    
          administrator : False

Unable to open libLLVM when building ZMQ

I am trying to set up a binder repo2docker environment which installs julia from conda-forge and makes it available as a jupyter kernel. (link to repo). As described in JuliaLang/IJulia.jl#717, this requires me to add the following to my postBuild script

julia -e 'ENV["JUPYTER"]="jupyter";
          using Pkg;
          Pkg.add("IJulia");
          Pkg.build("ZMQ")'

Building ZMQ leads to the following error:

Issue:

┌ Error: Error building `ZMQ`:
│ ERROR: LoadError: LoadError: Unable to open libLLVM!
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] (::getfield(BinaryProvider, Symbol("#open_libllvm#114")))() at /home/jovyan/.julia/packages/BinaryProvider/1nGWd/src/PlatformNames.jl:650
│  [3] detect_cxx11_string_abi() at /home/jovyan/.julia/packages/BinaryProvider/1nGWd/src/PlatformNames.jl:653
│  [4] detect_compiler_abi() at /home/jovyan/.julia/packages/BinaryProvider/1nGWd/src/PlatformNames.jl:666
│  [5] top-level scope at none:0
│  [6] include at ./boot.jl:317 [inlined]
│  [7] include_relative(::Module, ::String) at ./loading.jl:1041
│  [8] include at ./sysimg.jl:29 [inlined]
│  [9] include(::String) at /home/jovyan/.julia/packages/BinaryProvider/1nGWd/src/BinaryProvider.jl:1
│  [10] top-level scope at none:0
│  [11] include at ./boot.jl:317 [inlined]
│  [12] include_relative(::Module, ::String) at ./loading.jl:1041
│  [13] include(::Module, ::String) at ./sysimg.jl:29
│  [14] top-level scope at none:2
│  [15] eval at ./boot.jl:319 [inlined]
│  [16] eval(::Expr) at ./client.jl:389
│  [17] top-level scope at ./none:3
│ in expression starting at /home/jovyan/.julia/packages/BinaryProvider/1nGWd/src/PlatformNames.jl:683
│ in expression starting at /home/jovyan/.julia/packages/BinaryProvider/1nGWd/src/BinaryProvider.jl:12
│ ERROR: LoadError: Failed to precompile BinaryProvider [b99e7846-7c00-51b0-8f62-c81ae34c0232] to /home/jovyan/.julia/compiled/v1.0/BinaryProvider/ek6VZ.ji.
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] macro expansion at ./logging.jl:313 [inlined]
│  [3] compilecache(::Base.PkgId, ::String) at ./loading.jl:1187
│  [4] _require(::Base.PkgId) at ./logging.jl:311
│  [5] require(::Base.PkgId) at ./loading.jl:855
│  [6] macro expansion at ./logging.jl:311 [inlined]
│  [7] require(::Module, ::Symbol) at ./loading.jl:837
│  [8] include at ./boot.jl:317 [inlined]
│  [9] include_relative(::Module, ::String) at ./loading.jl:1041
│  [10] include(::Module, ::String) at ./sysimg.jl:29
│  [11] include(::String) at ./client.jl:388
│  [12] top-level scope at none:0
│ in expression starting at /home/jovyan/.julia/packages/ZMQ/ABGOx/deps/build.jl:1
└ @ Pkg.Operations /home/conda/feedstock_root/build_artifacts/julia_1539816087668/work/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1069

This is the same issue as JuliaPackaging/BinaryProvider.jl#130. There the suggested resolution was to not install julia from conda 😞. I would instead be happy if the conda version could be fixed.

Environment (conda list):

$ conda list
# packages in environment at /srv/conda:
#
# Name                    Version                   Build  Channel
affine                    2.2.1                      py_0    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
arpack                    3.5.0           blas_openblas_202  [blas_openblas]  conda-forge
asciitree                 0.3.3                      py_2    conda-forge
asn1crypto                0.24.0                   py36_3    conda-forge
attrs                     18.2.0                     py_0    conda-forge
automat                   0.7.0                      py_1    conda-forge
backcall                  0.1.0                      py_0    conda-forge
basemap                   1.2.0            py36h50ae964_0    conda-forge
blas                      1.1                    openblas    conda-forge
bleach                    2.1.4                      py_1    conda-forge
blinker                   1.4                        py_1    conda-forge
blosc                     1.14.4               hfc679d8_0    conda-forge
bokeh                     1.0.0                      py_0    pyviz/label/earthsim
boost                     1.66.0                   py36_1    conda-forge
boost-cpp                 1.66.0                        1    conda-forge
boto3                     1.9.33                     py_0    conda-forge
botocore                  1.12.33                    py_0    conda-forge
bottleneck                1.2.1            py36h7eb728f_1    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.10.15           ha4d7672_0    conda-forge
cachetools                2.1.0                      py_0    conda-forge
cairo                     1.14.12              he6fea26_5    conda-forge
cartopy                   0.16.0           py36hfa13621_0    defaults
certifi                   2018.10.15            py36_1000    conda-forge
cffi                      1.11.5           py36h5e8e0c9_1    conda-forge
cftime                    1.0.2.1          py36h7eb728f_0    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                        py_0    conda-forge
click-plugins             1.0.4                      py_0    conda-forge
cligj                     0.5.0                      py_0    conda-forge
cloudpickle               0.6.1                      py_0    conda-forge
colorcet                  1.0.0                      py_0    conda-forge
conda                     4.5.11                py36_1000    conda-forge
conda-env                 2.6.0                         1    defaults
configobj                 5.0.6                      py_0    conda-forge
constantly                15.1.0                     py_0    conda-forge
cryptography              2.3.1            py36hdffb7b8_0    conda-forge
cryptography-vectors      2.3.1                    py36_0    conda-forge
curl                      7.61.1               h74213dd_2    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cytoolz                   0.9.0.1          py36h470a237_1    conda-forge
dask                      0.20.0                     py_0    conda-forge
dask-core                 0.20.0                     py_0    conda-forge
dask-kubernetes           0.6.0                      py_0    conda-forge
datashader                0.6.9a1                    py_0    pyviz/label/earthsim
datashape                 0.5.4                    py36_0    conda-forge
dbus                      1.13.0               h3a4f0e9_0    conda-forge
decorator                 4.3.0                      py_0    conda-forge
defusedxml                0.5.0                    py36_0    conda-forge
descartes                 1.1.0                      py_2    conda-forge
distributed               1.24.0                py36_1000    conda-forge
docrep                    0.2.4                     <pip>
docutils                  0.14                  py36_1001    conda-forge
entrypoints               0.2.3                    py36_2    conda-forge
expat                     2.2.5                hfc679d8_2    conda-forge
fasteners                 0.14.1                     py_3    conda-forge
fftw                      3.3.8                h470a237_0    conda-forge
fiona                     1.7.13           py36hb00a9d7_4    conda-forge
fontconfig                2.13.0               h9420a91_0    defaults
freetype                  2.9.1                h6debe1e_4    conda-forge
freexl                    1.0.5                h470a237_2    conda-forge
future                    0.17.0                    <pip>
futures-compat            1.0                       py3_0    conda-forge
gcsfs                     0.1.2                      py_0    conda-forge
gdal                      2.2.4                    py36_0    pyviz/label/earthsim
geopandas                 0.4.0                      py_1    conda-forge
geos                      3.6.2                hfc679d8_3    conda-forge
geoviews                  1.6.0a1                    py_0    pyviz/label/earthsim
geoviews-core             1.6.0a1                    py_0    pyviz/label/earthsim
gettext                   0.19.8.1             h5e8e0c9_1    conda-forge
giflib                    5.1.4                h470a237_1    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
google-auth               1.5.1                      py_0    conda-forge
google-auth-oauthlib      0.1.0                    py36_0    conda-forge
graphite2                 1.3.12               hfc679d8_1    conda-forge
graphviz                  0.10.1                    <pip>
graphviz                  2.38.0               h08bfae6_9    conda-forge
gst-plugins-base          1.12.5               hde13a9d_0    conda-forge
gstreamer                 1.12.5               h61a6719_0    conda-forge
gsw                       3.2.1            py36h470a237_3    conda-forge
h5netcdf                  0.6.2                      py_0    conda-forge
h5py                      2.8.0            py36h7eb728f_3    conda-forge
harfbuzz                  1.9.0                h08d66d9_0    conda-forge
hdf4                      4.2.13               h951d187_2    conda-forge
hdf5                      1.10.2               hc401514_2    conda-forge
heapdict                  1.0.0                 py36_1000    conda-forge
holoviews                 1.11.0a9                   py_0    pyviz/label/earthsim
html5lib                  1.0.1                      py_0    conda-forge
hvplot                    0.2.1                      py_1    conda-forge
hyperlink                 17.3.1                     py_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
idna                      2.7                      py36_2    conda-forge
imageio                   2.3.0                      py_1    conda-forge
incremental               17.5.0                     py_0    conda-forge
intake                    0.2.9                      py_0    intake
intake-xarray             0.2.4                      py_0    intake
ipaddress                 1.0.22                    <pip>
ipykernel                 4.9.0                    py36_0    conda-forge
ipython                   6.5.0                    py36_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
jedi                      0.12.1                   py36_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
jmespath                  0.9.3                      py_1    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
json-c                    0.13.1               h470a237_1    conda-forge
jsonschema                2.6.0                    py36_2    conda-forge
julia                     1.0.1           blas_openblashfe40789_0  [blas_openblas]  conda-forge
jupyter                   1.0.0                      py_1    conda-forge
jupyter_client            5.2.3                      py_1    conda-forge
jupyter_console           5.2.0                    py36_1    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyterlab                0.35.3                   py36_0    conda-forge
jupyterlab_launcher       0.13.1                     py_2    conda-forge
jupyterlab_server         0.2.0                      py_0    conda-forge
kealib                    1.4.9                h0bee7d0_2    conda-forge
kiwisolver                1.0.1            py36h2d50403_2    conda-forge
krb5                      1.16.1               hbb41f41_0    conda-forge
libcurl                   7.61.1               hbdb9355_2    conda-forge
libdap4                   3.19.1                        0    conda-forge
libedit                   3.1.20170329         h6b74fdf_2    defaults
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 8.2.0                hdf63c60_1    defaults
libgdal                   2.2.4                h6f639c0_1    defaults
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libgit2                   0.27.7               h5ee2e84_0    conda-forge
libiconv                  1.15                 h470a237_3    conda-forge
libkml                    1.3.0                         6    pyviz/label/earthsim
libnetcdf                 4.6.1              h628ed10_200    conda-forge
libopenblas               0.3.3                h5a2b251_3    defaults
libpng                    1.6.35               ha92aebf_2    conda-forge
libpq                     10.5                 he29860b_0    conda-forge
libsodium                 1.0.16               h470a237_1    conda-forge
libspatialindex           1.8.5                hfc679d8_3    conda-forge
libspatialite             4.3.0a              he475c7f_19    defaults
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3    conda-forge
libtiff                   4.0.9                he6b73bb_2    conda-forge
libtool                   2.4.6                h470a237_2    conda-forge
libuuid                   1.0.3                         1    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
libxslt                   1.1.32               h88dbc4e_2    conda-forge
llvmlite                  0.25.0           py36hd28b015_1    conda-forge
locket                    0.2.0                      py_2    conda-forge
lxml                      4.2.5            py36hc9114bc_0    conda-forge
lz4                       1.1.0            py36h3b97293_1    conda-forge
lz4-c                     1.8.1.2                       0    conda-forge
markdown                  2.6.11                     py_0    conda-forge
markupsafe                1.0              py36h470a237_1    conda-forge
matplotlib                3.0.1                h8a2030e_1    conda-forge
matplotlib-base           3.0.1            py36hc039c98_1    conda-forge
metis                     5.1.0                h470a237_3    conda-forge
mistune                   0.8.3            py36h470a237_2    conda-forge
monotonic                 1.5                        py_0    conda-forge
mpfr                      4.0.1                h16a7912_0    conda-forge
msgpack-numpy             0.4.3.2                    py_0    conda-forge
msgpack-python            0.5.6            py36h2d50403_3    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
munch                     2.3.2                      py_0    conda-forge
nbconvert                 5.4.0                         0    conda-forge/label/broken
nbformat                  4.4.0                      py_1    conda-forge
nbserverproxy             0.8.5                   py_1000    conda-forge
ncurses                   6.1                  hfc679d8_1    conda-forge
netcdf4                   1.4.1           py36ha292673_200    conda-forge
networkx                  2.2                        py_1    conda-forge
nodejs                    10.8.0               hfc679d8_1    conda-forge
nomkl                     3.0                           0    defaults
notebook                  5.6.0                    py36_1    conda-forge
nteract-on-jupyter        1.9.6                     <pip>
numba                     0.40.0           py36hf8a1672_0    conda-forge
numcodecs                 0.5.5            py36hfc679d8_1    conda-forge
numpy                     1.15.3           py36h99e49ec_0    defaults
numpy-base                1.15.3           py36h2f8d375_0    defaults
oauthlib                  2.1.0                      py_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.2.20                        8    conda-forge
openjpeg                  2.3.0                h0e734dc_3    conda-forge
openlibm                  0.5.4                h470a237_0    conda-forge
openspecfun               0.5.3                h26a2512_0    conda-forge
openssl                   1.0.2p               h470a237_1    conda-forge
owslib                    0.17.0                     py_0    conda-forge
packaging                 18.0                       py_0    conda-forge
pandas                    0.23.4           py36hf8a1672_0    conda-forge
pandoc                    2.2.2                         1    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
panel                     0.2.0a2                    py_0    pyviz/label/earthsim
pango                     1.40.14              he752989_2    conda-forge
param                     1.8.1                      py_0    pyviz/label/earthsim
parso                     0.3.1                      py_0    conda-forge
partd                     0.3.9                      py_0    conda-forge
pcre                      8.42                 h439df22_0    defaults
pcre2                     10.23                         2    conda-forge
pexpect                   4.6.0                    py36_0    conda-forge
pickleshare               0.7.4                    py36_0    conda-forge
pillow                    5.3.0            py36hc736899_0    conda-forge
pip                       18.1                  py36_1000    conda-forge
pixman                    0.34.0               h470a237_3    conda-forge
poppler                   0.67.0               h4d7e492_3    conda-forge
poppler-data              0.4.9                         0    conda-forge
proj4                     5.0.1                         0    conda-forge
prometheus_client         0.3.0                      py_0    conda-forge
prompt_toolkit            1.0.15                     py_1    conda-forge
psutil                    5.4.7            py36h470a237_1    conda-forge
psycopg2                  2.7.5            py36hdffb7b8_2    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
ptyprocess                0.6.0                    py36_0    conda-forge
pyasn1                    0.4.4                      py_0    conda-forge
pyasn1-modules            0.2.1                      py_0    conda-forge
pycosat                   0.6.3            py36h470a237_1    conda-forge
pycparser                 2.18                       py_1    conda-forge
pyct                      0.4.4a10                   py_0    pyviz/label/earthsim
pyct-core                 0.4.4a10                   py_0    pyviz/label/earthsim
pyepsg                    0.3.2                      py_1    conda-forge
pygments                  2.2.0                      py_1    conda-forge
pyhamcrest                1.9.0                      py_2    conda-forge
pyjwt                     1.6.4                      py_0    conda-forge
pykdtree                  1.3.1            py36h7eb728f_2    conda-forge
pyopenssl                 18.0.0                   py36_0    conda-forge
pyparsing                 2.2.2                      py_0    conda-forge
pyproj                    1.9.5.1          py36h7b21b82_1    defaults
pyqt                      5.6.0            py36h8210e8a_7    conda-forge
pyresample                1.10.2           py36hf8a1672_0    conda-forge
pysal                     1.14.4.post2          py36_1001    conda-forge
pyshp                     1.2.12                     py_2    conda-forge
pysocks                   1.6.8                 py36_1002    conda-forge
python                    3.6.6                h5001a0f_3    conda-forge
python-blosc              1.4.4                    py36_0    conda-forge
python-dateutil           2.7.3                      py_0    conda-forge
python-kubernetes         4.0.0                    py36_1    conda-forge
python-snappy             0.5.3            py36h00d4201_0    conda-forge
pytz                      2018.7                     py_0    conda-forge
pyviz_comms               0.6.0                      py_0    conda-forge
pywavelets                1.0.1            py36h7eb728f_0    conda-forge
pyyaml                    3.13             py36h470a237_1    conda-forge
pyzmq                     17.1.2           py36hae99301_0    conda-forge
qt                        5.6.2                hf70d934_9    conda-forge
qtconsole                 4.4.2                      py_1    conda-forge
rasterio                  1.0.9            py36h1b5fcde_0    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
requests                  2.20.0                py36_1000    conda-forge
requests-oauthlib         0.8.0                    py36_1    conda-forge
rsa                       3.4.2                      py_1    conda-forge
rtree                     0.8.3                 py36_1000    conda-forge
ruamel_yaml               0.15.71          py36h470a237_0    conda-forge
s3transfer                0.1.13                py36_1001    conda-forge
scikit-image              0.14.1           py36hfc679d8_0    conda-forge
scipy                     1.1.0           py36_blas_openblas_200  [blas_openblas]  pyviz/label/earthsim
send2trash                1.5.0                      py_0    conda-forge
service_identity          17.0.0                     py_0    conda-forge
setuptools                40.2.0                   py36_0    conda-forge
shapely                   1.6.4            py36h164cb2d_1    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
sip                       4.18.1           py36hfc679d8_0    conda-forge
six                       1.11.0                   py36_1    conda-forge
snappy                    1.1.7                hfc679d8_2    conda-forge
snuggs                    1.4.1                      py_1    conda-forge
sortedcontainers          2.0.5                      py_0    conda-forge
sqlalchemy                1.2.12           py36h470a237_0    conda-forge
sqlite                    3.25.2               hb1c47c0_0    conda-forge
suitesparse               4.5.6           blas_openblash55dcaef_201  [blas_openblas]  conda-forge
tbb                       2019.1               h2d50403_0    conda-forge
tblib                     1.3.2                      py_1    conda-forge
terminado                 0.8.1                    py36_1    conda-forge
testpath                  0.3.1                    py36_1    conda-forge
tk                        8.6.8                         0    conda-forge
toolz                     0.9.0                      py_1    conda-forge
tornado                   4.5.3                    py36_0    conda-forge
traitlets                 4.3.2                    py36_0    conda-forge
twisted                   18.7.0           py36h470a237_1    conda-forge
urllib3                   1.23                  py36_1001    conda-forge
util-linux                2.21                          0    defaults
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          0.40.0                   py36_0    conda-forge
wheel                     0.31.1                   py36_1    conda-forge
widgetsnbextension        3.4.2                 py36_1000    conda-forge
xarray                    0.10.9                   py36_0    conda-forge
xarray                    0.10.9+49.g6d55f999           <pip>
xerces-c                  3.2.2                h5d6a6da_0    conda-forge
xgcm                      0.1.0                     <pip>
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                h470a237_4    conda-forge
xorg-libsm                1.2.2                h470a237_5    conda-forge
xorg-libx11               1.6.6                h470a237_0    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xorg-libxext              1.3.3                h470a237_4    conda-forge
xorg-libxpm               3.5.12               h470a237_2    conda-forge
xorg-libxrender           0.9.10               h470a237_2    conda-forge
xorg-libxt                1.1.5                h470a237_2    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
yaml                      0.1.7                had09818_2    defaults
zarr                      2.2.0                      py_1    conda-forge
zeromq                    4.2.5                hfc679d8_5    conda-forge
zict                      0.1.3                      py_0    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge
zope.interface            4.5.0            py36h470a237_1    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : None
       user config file : /home/jovyan/.condarc
 populated config files : /srv/conda/.condarc
          conda version : 4.5.11
    conda-build version : not installed
         python version : 3.6.6.final.0
       base environment : /srv/conda  (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 : /srv/conda/pkgs
                          /home/jovyan/.conda/pkgs
       envs directories : /srv/conda/envs
                          /home/jovyan/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.20.0 CPython/3.6.6 Linux/4.4.111+ ubuntu/18.04 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

[need input] stable release + experimental release

We simply cannot maintain this with dependencies changing all the time.

I propose the following:

• move julia output to a stable release mimicking almost exactly the upstream release (or even repackaging theirs)

• make a new output, name tbd (e.g. conda-julia or julia-cf or julia-ce) that will keep pushing the experimental enmeshing between conda and julia, including relaxing dependencies

Any input is appreciated.

---

• 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

Cannot add LibSSH2_jll

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

Issue:

When trying to add libSSH2_jll I get this error:

 ~ $ julia                                                                                                                                         (julia2) 
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.2 (2021-07-14)
 _/ |\__'_|_|_|\__'_|  |  conda-forge-julia release
|__/                   |

julia> import Pkg

julia> Pkg.add("LibSSH2_jll")
  Installing known registries into `~/.julia`
       Added registry `General` to `~/.julia/registries/General`
   Resolving package versions...
    Updating `~/.julia/environments/v1.6/Project.toml`
  [29816b5a] + LibSSH2_jll
    Updating `~/.julia/environments/v1.6/Manifest.toml`
  [56f22d72] + Artifacts
  [8f399da3] + Libdl
  [29816b5a] + LibSSH2_jll
  [c8ffd9c3] + MbedTLS_jll
Precompiling project...
  ✗ LibSSH2_jll
  1 dependency successfully precompiled in 4 seconds
  1 dependency errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the package

julia> import LibSSH2_jll
[ Info: Precompiling LibSSH2_jll [29816b5a-b9ab-546f-933c-edad1886dfa8]
ERROR: LoadError: InitError: could not load library "libmbedcrypto.so.5"
libmbedcrypto.so.5: cannot open shared object file: No such file or directory
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:114
  [2] dlopen (repeats 2 times)
    @ ./libdl.jl:114 [inlined]
  [3] __init__()
    @ MbedTLS_jll ~/mambaforge/envs/julia2/share/julia/stdlib/v1.6/MbedTLS_jll/src/MbedTLS_jll.jl:40
  [4] _include_from_serialized(path::String, depmods::Vector{Any})
    @ Base ./loading.jl:696
  [5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
    @ Base ./loading.jl:782
  [6] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1020
  [7] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:936
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:923
  [9] include
    @ ./Base.jl:386 [inlined]
 [10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1235
 [11] top-level scope
    @ none:1
 [12] eval
    @ ./boot.jl:360 [inlined]
 [13] eval(x::Expr)
    @ Base.MainInclude ./client.jl:446
 [14] top-level scope
    @ none:1
during initialization of module MbedTLS_jll
in expression starting at /home/izahn/mambaforge/envs/julia2/share/julia/stdlib/v1.6/LibSSH2_jll/src/LibSSH2_jll.jl:5
ERROR: Failed to precompile LibSSH2_jll [29816b5a-b9ab-546f-933c-edad1886dfa8] to /home/izahn/.julia/compiled/v1.6/LibSSH2_jll/jl_I1yS8u.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1385
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1329
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1043
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:936
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:923

Environment (conda list):

$ conda list
# packages in environment at /home/izahn/mambaforge/envs/julia2:
#
# 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                hbb0e23a_1    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

Details about conda and system ( conda info ):

$ conda info
     active environment : julia2
    active env location : /home/izahn/mambaforge/envs/julia2
            shell level : 2
       user config file : /home/izahn/.condarc
 populated config files : /home/izahn/mambaforge/.condarc
                          /home/izahn/.condarc
          conda version : 4.10.3
    conda-build version : 3.21.4
         python version : 3.9.7.final.0
       virtual packages : __linux=5.13.13=0
                          __glibc=2.33=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/izahn/mambaforge  (writable)
      conda av data dir : /home/izahn/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
                          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/izahn/mambaforge/pkgs
                          /home/izahn/.conda/pkgs
       envs directories : /home/izahn/mambaforge/envs
                          /home/izahn/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.7 Linux/5.13.13-arch1-1 arch/rolling glibc/2.33
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

pre-unlink.sh and juliarc.jl are out of date

pre-unlink.sh and juliarc.jl are out of date

pre-unlink.sh refers to JULIA_PKGDIR which has been replaced by JULIA_DEPOT_PATH
juliarc.jl should be now be ~/.julia/config/startup.jl since Julia v0.7

Going forward the best way to manage conda environments and julia environments would to create a new top-level shared julia environment for each conda environment. This has become easier with certain command line changes:

https://docs.julialang.org/en/v1/NEWS/#Command-line-option-changes

Release 0.6.0

Not sure all what this will entail, but would be great if we could package 0.6.0 as well. If we want to support multiple versions (e.g. 0.5 and 0.6), we can create a branch for 0.5 that can see continued maintenance and just add 0.6.0 to master.

packaging Julia packages for conda-forge

My second concern is that it is not completely clear to me to what degree this PR really addresses the issues it closes. For example, #14 is about packaging Julia packages for conda-forge, i.e. how should I create the conda-forge feedstock julia-rainfarm from https://github.com/jhardenberg/RainFARM.jl. While sorting out the depot paths certainly helps and might be necessary, from reading this PR I still don't know how to do this or where to look up the documentation. In terms of documentation, at a minimum I would expect a bullet point in the enumeration for new packages.

This is probably beyond the scope of this PR, but in that case we might want to keep #14 open for now.

Originally posted by @zklaus in #157 (comment)

Pull pcre2 from conda-forge

When pcre2 has been accepted into conda-forge, add it as a build-time and run-time requirement

conda-forge/staged-recipes#3656

[need help] tracking windows, arm64, aarch64, ppc64le builds

We plan to build for windows, arm64, aarch64, and ppc64le soon. This issue is a central place to track the development on that front. More details soon once we get some other work out of the way.

---

TODO:

• windows (#168)
• arm64
• aarch
• ppc

---

Current known bottlenecks on the arm/aarch front:

• openlibm (clear!)
• mbedtls (https://github.com/conda-forge/mbedtls-feedstock)
• openblas-ilp64 (starting point: #157 (comment) and see this: conda-forge/openblas-feedstock#131)
• p7zip (conda-forge/p7zip-feedstock#2 and conda-forge/p7zip-feedstock#3)

---

• 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

Suggestion to use the pre-built julia binaries

I would like to make a suggestion. Instead of building from source, is it possible for this package to use the binaries provided by the julia project? We go through a lot of effort in patching and producing julia binaries that work on all platforms correctly.

Thus just downloading these binaries from julialang.org and untarring them would give the most reliable installation of Julia that is possible for the upstream to support.

Warning related to JULIA_PKGDIR seen during update

Issue: julia returned a warning during my most recent conda update.

Here's the warning returned to my console:

Preparing transaction: done
Verifying transaction: done
Executing transaction: | ERROR: KeyError: key "JULIA_PKGDIR"                                                           $
Stacktrace:
 [1] (::getfield(Base, Symbol("##418#419")))(::String) at ./                                                           $
 [2] access_env at ./env.jl:45 [inlined]
 [3] getindex(::Base.EnvDict, ::String) at ./env.jl:76
 [4] top-level scope at none:0

WARNING conda.core.link:run_script(818): pre-unlink script f                                                           $
consider notifying the package maintainer                |   Updating registry at `~/.julia/registries/Gene            $
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
    Fetching: [>                                        ]  0.0 %
    Resolving Deltas: [==============================>          ]  72.5 %
 Resolving package versions...
                                                                                                         do            $

Environment (conda list):

$ conda list

# Name                    Version                   Build  Channel
alabaster                 0.7.12                     py_0    conda-forge
anaconda                  custom           py36hbbc8b67_0
anaconda-client           1.7.1                      py_0    conda-forge
anaconda-project          0.8.2                      py_1    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
arpack                    3.6.3           blas_openblash77d739c_2  [blas_openblas]  conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
astroid                   2.1.0                 py36_1000    conda-forge
astropy                   3.1.1            py36h470a237_0    conda-forge
atk                       2.25.90              h05f3006_1    conda-forge
atomicwrites              1.2.1                      py_0    conda-forge
attrs                     18.2.0                     py_0    conda-forge
automat                   0.7.0                      py_1    conda-forge
babel                     2.6.0                      py_1    conda-forge
backcall                  0.1.0                      py_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.os              0.1.1                 py36_1000    conda-forge
backports.shutil_get_terminal_size 1.0.0                      py_3    conda-forge
bcftools                  1.9                  h4da6232_0    bioconda
beautifulsoup4            4.7.0                 py36_1000    conda-forge
bedtools                  2.27.1               he941832_2    bioconda
bitarray                  0.8.3            py36h470a237_0    conda-forge
bkcharts                  0.2                      py36_0    conda-forge
blas                      1.1                    openblas    conda-forge
blaze                     0.11.3                   py36_0    conda-forge
bleach                    3.0.2                      py_1    conda-forge
blinker                   1.4                        py_1    conda-forge
blosc                     1.15.1               hfc679d8_0    conda-forge
bokeh                     1.0.3                 py36_1000    conda-forge
boto                      2.49.0                     py_0    conda-forge
boto3                     1.9.72                     py_0    conda-forge
botocore                  1.12.73                    py_0    conda-forge
bottleneck                1.2.1            py36h7eb728f_1    conda-forge
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.12              h276e583_5    conda-forge
certifi                   2018.11.29            py36_1000    conda-forge
cffi                      1.11.5           py36h5e8e0c9_1    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                        py_0    conda-forge
cloudpickle               0.6.1                      py_0    conda-forge
clyent                    1.2.2                      py_1    conda-forge
colorama                  0.4.1                      py_0    conda-forge
constantly                15.1.0                     py_0    conda-forge
contextlib2               0.5.5                      py_2    conda-forge
cryptography              2.2.1            py36hdffb7b8_1    conda-forge
cryptography-vectors      2.4.2                   py_1000    conda-forge
curl                      7.63.0               h74213dd_0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cython                    0.29.2           py36hfc679d8_0    conda-forge
cytoolz                   0.9.0.1          py36h470a237_1    conda-forge
dask                      1.0.0                      py_0    conda-forge
dask-core                 1.0.0                      py_0    conda-forge
datashape                 0.5.4                    py36_0    conda-forge
dbus                      1.13.0               h3a4f0e9_0    conda-forge
decorator                 4.3.0                      py_0    conda-forge
deeptools                 3.1.3            py36h470a237_0    bioconda
defusedxml                0.5.0                      py_1    conda-forge
distributed               1.25.1                py36_1000    conda-forge
docutils                  0.14                  py36_1001    conda-forge
emacs                     26.1                 h5d2cb88_0    conda-forge
entrypoints               0.2.3                 py36_1002    conda-forge
et_xmlfile                1.0.1                    py36_0    conda-forge
expat                     2.2.5                hfc679d8_2    conda-forge
fastcache                 1.0.2            py36h470a237_1    conda-forge
fftw                      3.3.8                h470a237_1    conda-forge
filelock                  3.0.10                     py_0    conda-forge
flask                     1.0.2                      py_2    conda-forge
flask-cors                3.0.7                      py_0    conda-forge
fontconfig                2.13.1               h65d0f4c_0    conda-forge
freetype                  2.9.1                h6debe1e_4    conda-forge
fribidi                   1.0.5                h470a237_0    conda-forge
gdk-pixbuf                2.36.12              h4ab6910_1    conda-forge
gensim                    3.5.0                    py36_0    conda-forge
get_terminal_size         1.0.0                haa9412d_0
gettext                   0.19.8.1             h5e8e0c9_1    conda-forge
gevent                    1.3.7            py36h470a237_0    conda-forge
giflib                    5.1.4                h470a237_1    conda-forge
glib                      2.56.2               h464dc38_1    conda-forge
glob2                     0.6                        py_0    conda-forge
gmp                       6.1.2                hfc679d8_0    conda-forge
gmpy2                     2.0.8            py36hb705a9b_2    conda-forge
gnutls                    3.6.5                ha0399c4_1    conda-forge
gobject-introspection     1.56.1           py36haaf12d0_1    conda-forge
graphite2                 1.3.13               hfc679d8_0    conda-forge
greenlet                  0.4.13                   py36_0    conda-forge
gst-plugins-base          1.12.5               hde13a9d_0    conda-forge
gstreamer                 1.12.5               h5856ed1_0    conda-forge
gtk2                      2.24.31              hde048ef_0    conda-forge
h5py                      2.9.0            py36he5c79e1_0    conda-forge
harfbuzz                  1.9.0                h04dbb29_1    conda-forge
hdf5                      1.10.4          nompi_h5598ddc_1105    conda-forge
heapdict                  1.0.0                 py36_1000    conda-forge
homer                     4.9.1           pl526h2d50403_6    bioconda
html5lib                  1.0.1                      py_0    conda-forge
htslib                    1.9                  hc238db4_4    bioconda
hyperlink                 17.3.1                     py_0    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
idna                      2.8                   py36_1000    conda-forge
imageio                   2.4.1                 py36_1000    conda-forge
imagesize                 1.1.0                      py_0    conda-forge
importlib_metadata        0.6                      py36_0    conda-forge
incremental               17.5.0                     py_0    conda-forge
intel-openmp              2019.1                      144
ipykernel                 5.1.0           py36h24bf2e0_1001    conda-forge
ipython                   7.2.0           py36h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
isort                     4.3.4                 py36_1000    conda-forge
itsdangerous              1.1.0                      py_0    conda-forge
jbig                      2.1               h470a237_1001    conda-forge
jdcal                     1.4                        py_1    conda-forge
jedi                      0.13.2                py36_1000    conda-forge
jeepney                   0.4                        py_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
jmespath                  0.9.3                      py_1    conda-forge
jpeg                      9c                   h470a237_1    conda-forge
jsonschema                3.0.0a3               py36_1000    conda-forge
julia                     1.0.3           blas_openblash977ebb0_0  [blas_openblas]  conda-forge
jupyter                   1.0.0                      py_1    conda-forge
jupyter_client            5.2.4                      py_0    conda-forge
jupyter_console           6.0.0                      py_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyterlab                0.35.4                   py36_0    conda-forge
jupyterlab_launcher       0.13.1                     py_2    conda-forge
jupyterlab_server         0.2.0                      py_0    conda-forge
keyring                   17.1.1                py36_1000    conda-forge
kiwisolver                1.0.1            py36h2d50403_2    conda-forge
krb5                      1.16.2               hbb41f41_0    conda-forge
lazy-object-proxy         1.3.1            py36h470a237_0    conda-forge
libcurl                   7.63.0               hbdb9355_0    conda-forge
libdeflate                1.0                  h470a237_0    bioconda
libedit                   3.1.20170329         haf1bffa_1    conda-forge
libevent                  2.0.22               hdffb7b8_2    conda-forge
libffi                    3.2.1                hfc679d8_5    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libgit2                   0.27.7               h5ee2e84_0    conda-forge
libiconv                  1.15                 h470a237_3    conda-forge
libopenblas               0.2.20               h9ac9557_7
libpng                    1.6.36               ha92aebf_0    conda-forge
libsodium                 1.0.16               h470a237_1    conda-forge
libssh2                   1.8.0                h5b517e9_3    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3    conda-forge
libtiff                   4.0.10               he6b73bb_1    conda-forge
libtool                   2.4.6                h470a237_2    conda-forge
libuuid                   2.32.1               h470a237_2    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_5    conda-forge
libxslt                   1.1.32               h88dbc4e_2    conda-forge
llvmlite                  0.26.0           py36hd28b015_0    conda-forge
locket                    0.2.0                      py_2    conda-forge
lxml                      4.2.5            py36hc9114bc_0    conda-forge
lzo                       2.10                 h470a237_0    conda-forge
markupsafe                1.1.0            py36h470a237_0    conda-forge
matplotlib                3.0.2            py36h8a2030e_1    conda-forge
matplotlib-base           3.0.2            py36h20b835b_1    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
metis                     5.1.0                hfc679d8_3    conda-forge
mistune                   0.8.4            py36h470a237_0    conda-forge
mkl                       2019.1                      144
mkl-service               1.1.2            py36h651fb7a_4
mkl_fft                   1.0.10                   py36_0    conda-forge
mkl_random                1.0.2                    py36_0    conda-forge
more-itertools            4.3.0                 py36_1000    conda-forge
mpc                       1.1.0                hb705a9b_6    conda-forge
mpfr                      4.0.1                h16a7912_0    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
msgpack-python            0.6.0            py36h2d50403_0    conda-forge
multipledispatch          0.6.0                      py_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1                  hfc679d8_2    conda-forge
nettle                    3.4.1                h470a237_2    conda-forge
networkx                  2.2                        py_1    conda-forge
nltk                      3.2.5                      py_0    conda-forge
nose                      1.3.7                 py36_1002    conda-forge
notebook                  5.7.4                 py36_1000    conda-forge
numba                     0.41.0           py36hf8a1672_0    conda-forge
numexpr                   2.6.9            py36hf8a1672_0    conda-forge
numpy                     1.15.4          py36_blas_openblashb06ca3d_0  [blas_openblas]  conda-forge
numpy-base                1.14.3           py36h0ea5e3f_1
numpydoc                  0.8.0                      py_1    conda-forge
oauthlib                  2.1.0                      py_0    conda-forge
odo                       0.5.1                      py_1    conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.3.3                ha44fe06_1    conda-forge
openlibm                  0.5.4                h470a237_0    conda-forge
openpyxl                  2.5.12                     py_0    conda-forge
openspecfun               0.5.3                h26a2512_0    conda-forge
openssl                   1.0.2p               h470a237_2    conda-forge
packaging                 18.0                       py_0    conda-forge
pandas                    0.23.4           py36hf8a1672_0    conda-forge
pandoc                    2.5                           0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.40.14              he752989_2    conda-forge
parso                     0.3.1                      py_0    conda-forge
partd                     0.3.9                      py_0    conda-forge
patchelf                  0.9                  hfc679d8_2    conda-forge
path.py                   11.5.0                     py_0    conda-forge
pathlib2                  2.3.3                 py36_1000    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.41                 hfc679d8_3    conda-forge
pcre2                     10.23                         2    conda-forge
pep8                      1.7.1                      py_0    conda-forge
perl                      5.26.2               h470a237_0    conda-forge
pexpect                   4.6.0                 py36_1000    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pillow                    5.4.0            py36hc736899_0    conda-forge
pip                       18.1                  py36_1000    conda-forge
pixman                    0.34.0               h470a237_3    conda-forge
pkginfo                   1.4.2                      py_1    conda-forge
plotly                    3.4.2                      py_0    conda-forge
pluggy                    0.8.0                      py_0    conda-forge
ply                       3.11                       py_1    conda-forge
prometheus_client         0.5.0                      py_0    conda-forge
prompt_toolkit            2.0.7                      py_0    conda-forge
psutil                    5.4.8            py36h470a237_0    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
ptyprocess                0.6.0                 py36_1000    conda-forge
py                        1.7.0                      py_0    conda-forge
py2bit                    0.3.0                    py36_1    bioconda
pyasn1                    0.4.4                      py_1    conda-forge
pyasn1-modules            0.2.3                      py_0    conda-forge
pybigwig                  0.3.12           py36hdfb72b2_2    bioconda
pycodestyle               2.4.0                      py_1    conda-forge
pycosat                   0.6.3            py36h470a237_1    conda-forge
pycparser                 2.19                       py_0    conda-forge
pycrypto                  2.6.1            py36h470a237_2    conda-forge
pycurl                    7.43.0.2         py36hb7f436b_0
pyflakes                  2.0.0                      py_0    conda-forge
pygments                  2.3.1                      py_0    conda-forge
pyhamcrest                1.9.0                      py_2    conda-forge
pyjwt                     1.7.1                      py_0    conda-forge
pylint                    2.2.2                 py36_1000    conda-forge
pyodbc                    4.0.24           py36hfc679d8_0    conda-forge
pyopenssl                 18.0.0                py36_1000    conda-forge
pyparsing                 2.3.0                      py_0    conda-forge
pyqt                      5.6.0            py36h8210e8a_8    conda-forge
pyrsistent                0.14.8           py36h470a237_0    conda-forge
pysam                     0.15.1           py36h0380709_0    bioconda
pysocks                   1.6.8                 py36_1002    conda-forge
pytables                  3.4.4            py36h72a6d90_4    conda-forge
pytest                    4.0.2                 py36_1000    conda-forge
pytest-arraydiff          0.3                        py_0    conda-forge
pytest-astropy            0.4.0                      py_0    conda-forge
pytest-doctestplus        0.1.3                      py_0    conda-forge
pytest-openfiles          0.3.1                      py_0    conda-forge
pytest-remotedata         0.3.1                      py_0    conda-forge
python                    3.6.7                h5001a0f_1    conda-forge
python-crfsuite           0.9.6            py36h2d50403_0    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
pytz                      2018.7                     py_0    conda-forge
pywavelets                1.0.1            py36h7eb728f_0    conda-forge
pyyaml                    3.13             py36h470a237_1    conda-forge
pyzmq                     17.1.2           py36hae99301_1    conda-forge
qt                        5.6.2               h679f5bc_11    conda-forge
qtawesome                 0.5.5              pyh8a2030e_0    conda-forge
qtconsole                 4.4.3                      py_0    conda-forge
qtpy                      1.5.2              pyh8a2030e_0    conda-forge
readline                  7.0                  haf1bffa_1    conda-forge
requests                  2.21.0                py36_1000    conda-forge
requests-oauthlib         1.0.0                      py_1    conda-forge
retrying                  1.3.3                      py_2    conda-forge
rope                      0.10.7                     py_1    conda-forge
ruamel_yaml               0.15.71          py36h470a237_0    conda-forge
s3transfer                0.1.13                py36_1001    conda-forge
samtools                  1.9                  h8ee4bcc_1    bioconda
scikit-image              0.14.1           py36hfc679d8_3    conda-forge
scikit-learn              0.20.2          py36_blas_openblash00c3548_400  [blas_openblas]  conda-for             ge
scipy                     1.2.0           py36_blas_openblashb06ca3d_200  [blas_openblas]  conda-for             ge
seaborn                   0.9.0                      py_0    conda-forge
secretstorage             3.1.0                 py36_1001    conda-forge
send2trash                1.5.0                      py_0    conda-forge
service_identity          17.0.0                     py_0    conda-forge
setuptools                40.6.3                   py36_0    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
singledispatch            3.4.0.3               py36_1000    conda-forge
sip                       4.18.1           py36hfc679d8_0    conda-forge
six                       1.12.0                py36_1000    conda-forge
smart_open                1.7.1                      py_0    conda-forge
snappy                    1.1.7                hfc679d8_2    conda-forge
snowballstemmer           1.2.1                      py_1    conda-forge
sortedcollections         1.0.1                      py_1    conda-forge
sortedcontainers          2.1.0                      py_0    conda-forge
sphinx                    1.8.3                 py36_1000    conda-forge
sphinxcontrib             1.0                      py36_1
sphinxcontrib-websupport  1.1.0                      py_1    conda-forge
spyder                    3.3.2                 py36_1001    conda-forge
spyder-kernels            0.3.0                 py36_1001    conda-forge
sqlalchemy                1.2.15           py36h470a237_0    conda-forge
sqlite                    3.26.0               hb1c47c0_0    conda-forge
statsmodels               0.9.0            py36h7eb728f_0    conda-forge
suitesparse               4.5.6           blas_openblash697e320_201  [blas_openblas]  conda-forge
sympy                     1.3                   py36_1000    conda-forge
tbb                       2019.3               h2d50403_0    conda-forge
tblib                     1.3.2                      py_1    conda-forge
terminado                 0.8.1                 py36_1001    conda-forge
testpath                  0.4.2                 py36_1000    conda-forge
tk                        8.6.9                ha92aebf_0    conda-forge
tmux                      2.7                  hc78d2af_3    conda-forge
toolz                     0.9.0                      py_1    conda-forge
tornado                   5.1.1            py36h470a237_0    conda-forge
tqdm                      4.28.1                     py_0    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
twisted                   18.9.0           py36h470a237_0    conda-forge
twython                   3.7.0                      py_0    conda-forge
typed-ast                 1.1.1            py36h470a237_0    conda-forge
umap-learn                0.3.7                 py36_1000    conda-forge
unicodecsv                0.14.1                     py_1    conda-forge
unixodbc                  2.3.7                h09ba92c_0    conda-forge
urllib3                   1.24.1                py36_1000    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
werkzeug                  0.14.1                     py_0    conda-forge
wheel                     0.32.3                   py36_0    conda-forge
widgetsnbextension        3.4.2                 py36_1000    conda-forge
wrapt                     1.10.11          py36h470a237_1    conda-forge
wurlitzer                 1.0.2                 py36_1000    conda-forge
xlrd                      1.2.0                      py_0    conda-forge
xlsxwriter                1.1.2                      py_0    conda-forge
xlwt                      1.3.0                      py_1    conda-forge
xorg-fixesproto           5.0                  h470a237_2    conda-forge
xorg-kbproto              1.0.7                h470a237_2    conda-forge
xorg-libice               1.0.9                h470a237_4    conda-forge
xorg-libsm                1.2.3                h8c8a85c_0    conda-forge
xorg-libx11               1.6.6                h470a237_0    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxaw               1.0.13               h470a237_2    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xorg-libxext              1.3.3                h470a237_4    conda-forge
xorg-libxfixes            5.0.3                h470a237_4    conda-forge
xorg-libxft               2.3.2                h7c24a56_3    conda-forge
xorg-libxmu               1.1.2                h470a237_2    conda-forge
xorg-libxpm               3.5.12               h470a237_2    conda-forge
xorg-libxrender           0.9.10               h470a237_2    conda-forge
xorg-libxt                1.1.5                h470a237_2    conda-forge
xorg-renderproto          0.11.1               h470a237_2    conda-forge
xorg-xextproto            7.3.0                h470a237_2    conda-forge
xorg-xproto               7.0.31               h470a237_7    conda-forge
xz                        5.2.4                h470a237_1    conda-forge
yaml                      0.1.7                h470a237_1    conda-forge
zeromq                    4.2.5                hfc679d8_6    conda-forge
zict                      0.1.3                      py_0    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge
zope                      1.0                      py36_1
zope.interface            4.6.0            py36h470a237_0    conda-forge

Details about conda and system ( conda info ):

$ conda info

     active environment : bioinfo
    active env location : /home/bioinfo/.conda/envs/bioinfo
            shell level : 2
       user config file : /home/bioinfo/.condarc
 populated config files : /home/bioinfo/.condarc
          conda version : 4.5.12
    conda-build version : not installed
         python version : 3.6.8.final.0
       base environment : /usr/local/bin/miniconda3  (read only)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/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 : /usr/local/bin/miniconda3/pkgs
                          /home/bioinfo/.conda/pkgs
       envs directories : /home/bioinfo/.conda/envs
                          /usr/local/bin/miniconda3/envs
               platform : linux-64
             user-agent : conda/4.5.12 requests/2.21.0 CPython/3.6.8 Linux/3.10.0-957.1.3.el7.x86_64 rhel/7.6 glibc/2.17
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False

Newest build of julia 1.6 (from yesterday) appears to be broken.

Julia seems to be looking for PREFIX/lib/julia/libopenlibm.so which does not exist.

julia upgrade: pre-unlink script failed warning

  - julia                      1.6.4  h2a39549_0              installed                      
  + julia                      1.6.4  h34dcedf_2              conda-forge/linux-64      96 MB

  - libunwind                  1.6.2  h9c3ff4c_0              installed                      
  + libunwind                  1.5.0  h9c3ff4c_1              conda-forge/linux-64      72 KB

WARNING conda.core.link:run_script(1228): pre-unlink script failed for package conda-forge/linux-64::julia-1.6.4-h2a39549_0
consider notifying the package maintainer

• 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

Use conda-forge's openlibm

As openlibm is being added as a package in conda-forge ( conda-forge/staged-recipes#3959 ), we should make it a dependency instead of having julia build its own copy. Given that any build of julia uses a specific version of openlibm and we are unsure of the ABI compatibility, we should pin exactly what version of openlibm we use. Once the ABI is known (and is determined to be stable), we can revisit how we pin this dependency.

binary compatibility between conda and julia

The issue of separate depots for separate environments is really all about binary compatibility. Basically, anything that has been compiled for one environment cannot reliably be used with another environment because linked libraries may have changed in an ABI incompatible way (cf the recent libunwind problems, but I would expect this with a number of libraries, e.g. for I/O of special file formats like netCDF) and the compilers themselves may be different. If compiled bits are shared, this will lead to surprising segfaults in the future. This kind of problem is not likely to show up in tests that use similar environments created at roughly the same time, but is virtually guaranteed if very different environments with library overlap are used, particularly when those environments are created a long time apart.

To me, it is not clear to what degree compiled bits are an integral part of the Julia depots, but this is my main problem with ~/.julia currently (i.e. conda-forge Julia <=1.6).

Originally posted by @zklaus in #157 (comment)

start a dev branch

This will help us diagnose issues and borrow patches as necessary.

• 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

Windows build

I've started to look at setting up ijulia on windows, and this would be a really nice option to help get Julia considering that I already use conda.

Mock label for "bring your own julia"

Since we have put some effort into activate.sh to enhance integration between conda and Julia, perhaps we should consider a mock package the only delivers the scripts, but not the binaries.

The environment variables that we set would affect a Julia installed from another mechanism. juliaup is one example. This would allow us to provide the benefits of activate.sh while also allowing a wider source of Julia installs to take advantage of them. For example, this would help Windows users currently for which we currently cannot build Julia due to lack of dependencies or a modern MSYS2 build environment to use.

integration with Conda.jl?

If someone uses the conda-forge Julia with the Conda.jl package (e.g. this is the default configuration for PyCall and PyPlot on Windows and Mac), it would be nice if Conda.jl automatically realized this and used the same conda environment instead of installing its own?

Is there a good way to detect this when Conda.jl is running its build script? i.e. how can we detect if we are running Julia via conda-forge?

Question: Why PREFIX and not CONDA_PREFIX?

This isn't really an issue, just a question: in the build script of the recipe, the environment variable PREFIX appears to be used to refer to the directory of the current conda environment.

However, I thought that the corresponding environment variable is CONDA_PREFIX. At the very least, when I do something like conda activate test, then echo $PREFIX leads to no output, but echo $CONDA_PREFIX gives the directory of the conda environment.

Is this perhaps a platform-specific issue? I am on Mac OS X, not Linux. (Although this is also true on the Linux workstation where I work.)

To be honest I don't really understand the relevant conda documentation on the issue:

https://conda.io/docs/user-guide/tasks/build-packages/environment-variables.html

PREFIX | Build prefix to which the build script should install.
CONDA_PREFIX | The path to the conda environment used to build the package, such as /path/to/conda/env. Useful to pass as the environment prefix parameter to various conda tools, usually labeled -p or --prefix.

My hope was that you might be able to clarify this in the context of the build script for this recipe.

Build failures due to libgit2/SSL error

I've been unable to build this recipe locally (CentOS 7, conda-build 2.1.18) due to julia's libgit2 failing to connect to github over HTTPS with an 'invalid certificate' error.

Possibly related issues:

JuliaLang/julia#13399
JuliaLang/julia#17789
JuliaLang/julia#15128

Possibly related to this commit:

JuliaLang/julia@87913c6

Update Julia version

0.6.2 is not included

Failing to install julia-1.6.4: Segmentation fault

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

Issue:

I am trying to install julia into a clean conda environment using conda install -c conda-forge julia=1.6.4, but I am getting:

...
Preparing transaction: done
Verifying transaction: done
Executing transaction: |
done
ERROR conda.core.link:_execute(699): An error occurred while installing package 'conda-forge::julia-1.6.4-h2a39549_0'.
Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::julia-1.6.4-h2a39549_0
location of failed script: /home/gerd-jln/.conda/envs/condatesting/bin/.julia-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: /home/gerd-jln/.conda/envs/condatesting/bin/.julia-post-link.sh: line 1: 66209 Segmentation fault      (core dumped) "${PREFIX}/bin/julia" -e 'using Pkg; Pkg.instantiate()' >> "${PREFIX}/.messages.txt" 2>&1

return code: 139

()

Environment (conda list):

$ conda list
# packages in environment at /home/gerd-jln/.conda/envs/condatesting:
#
# Name                    Version                   Build  Channel

Details about conda and system ( conda info ):

$ conda info

     active environment : condatesting
    active env location : /home/gerd-jln/.conda/envs/condatesting
            shell level : 1
       user config file : /home/gerd-jln/.condarc
 populated config files : /usr/share/conda/condarc.d/defaults.yaml
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.10.0.final.0
       virtual packages : __linux=5.15.4=0
                          __glibc=2.34=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /usr  (read only)
      conda av data dir : /usr/etc/conda
  conda av metadata url : None
           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 : /var/cache/conda/pkgs
                          /home/gerd-jln/.conda/pkgs
       envs directories : /home/gerd-jln/.conda/envs
                          /usr/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.10.0 Linux/5.15.4-201.fc35.x86_64 fedora/35 glibc/2.34
                UID:GID : 1000:1000
             netrc file : /home/gerd-jln/.netrc
           offline mode : False

Skip building HTML docs

Seems that Julia is building the HTML docs as part of the build by default. Not sure that we want to include these. Pretty easy to find them online or download them. Also doubt that someone go looking for them in the conda package. Further this step involves creating a Python virtualenv environment, downloading a bunch of dependencies, and then doing this build. Seems like that time could be better spent. That said, it is not totally clear how to skip this step except for patching the Makefile or letting it run through and deleting the docs after the fact. Would be good to figure out the best way to approach this.

libgit issues with Julia 1.6.5 h989b2f6_0

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

Set JULIA_SSL_CA_ROOTS_PATH

Julia is not locating the conda-forge ca-certificates.

julia> using NetworkOptions

julia> NetworkOptions.ca_roots()
"/etc/ssl/certs/ca-certificates.crt"

We should set

JULIA_SSL_CA_ROOTS_PATH=$CONDA_PREFIX/ssl/cacert.pem

then

julia> using NetworkOptions

julia> NetworkOptions.ca_roots()
"/home/mkitti/anaconda3/envs/julia171_test/ssl/cacert.pem"

julia> ENV["JULIA_SSL_CA_ROOTS_PATH"]
"/home/mkitti/anaconda3/envs/julia171_test/ssl/cacert.pem"

Pulling out Julia's patched LLVM

One thing we might want to start considering is pulling out Julia's patched LLVM portion as a separate package. Building LLVM alone takes a lot of time. As such we may start encountering difficulties building Julia outside of CircleCI where time limits are more stringent or for later versions of Julia.

If we can create a separate package for Julia's LLVM build possibly using the llvmdev package and an llvm_variant, we should be able to rely on that package for the build (and run?). Doing this should allow us to cutdown the build time here and also draw on the expertise we have here at conda-forge. This will require coordination with the @conda-forge/llvmdev team and @SylvainCorlay's guidance in particular as he developed the llvm_variant system.

Latest Version of Julia

Please provide the latest version of Julia, instead of just 1.1

CondaPkg.jl integration

There is a new package that is an independent implementation distinct from Conda.jl called CondaPkg.jl.

The corresponding interop issue on CondaPkg.jl is here:
JuliaPy/CondaPkg.jl#19

In particular, the latest version adds a conda command to the julia pkg repl mode:
https://discourse.julialang.org/t/ann-condapkg-jl-v0-2-6-now-with-repl-integration/75370

Pull dSFMT from conda-forge

I've opened conda-forge/staged-recipes#3965 to add dSFMT to conda-forge.

We'll need to take a look at a few files in the julia repo to match their build:

https://github.com/JuliaLang/julia/blob/master/deps/dsfmt.mk
https://github.com/JuliaLang/julia/blob/master/deps/libdSFMT.def
https://github.com/JuliaLang/julia/blob/master/deps/patches/dSFMT.h.patch
https://github.com/JuliaLang/julia/blob/master/deps/patches/dSFMT.c.patch

Release 0.6.1

Julia 0.6.1 was released a few days ago.

libgit2 dependency

I'm not sure if this is the correct place to report the issue (I couldn't even find the actual recipe, otherwise I'd have made a pull request directly). Actually, I'm not sure if there's need to make any changes... but here I am to report that I couldn't install julia without installing libgit2 beforehand at my conda environment. Dependency should be added.

$ conda install julia
Fetching package metadata .................
Solving package specifications: .

Package plan for installation in environment /home/kzkt/tools/infobio:

The following NEW packages will be INSTALLED:

    arpack:       3.5.0-blas_openblas_201 conda-forge [blas_openblas]
    blas:         1.1-openblas            conda-forge
    fftw:         3.3.6-3                 conda-forge
    gmp:          6.1.2-0                 conda-forge
    julia:        0.6.0-blas_openblas_200 conda-forge [blas_openblas]
    libgit2:      0.25.1-0                conda-forge
    libssh2:      1.8.0-1                 conda-forge
    metis:        5.1.0-3                 conda-forge
    mpfr:         3.1.5-0                 conda-forge
    openblas:     0.2.19-2                conda-forge
    openlibm:     0.5.4-0                 conda-forge
    openspecfun:  0.5.3-0                 conda-forge
    pcre2:        10.21-3                 conda-forge
    suitesparse:  4.5.4-blas_openblas_200 conda-forge [blas_openblas]
    tbb:          4.4_20150728-0          bioconda   

The following packages will be UPDATED:

    anaconda:     4.4.0-np112py36_0                   --> custom-py36hbbc8b67_0                    
    gsl:          2.1-2                   conda-forge --> 2.2.1-blas_openblas_2         conda-forge [blas_openblas]
    numpy:        1.12.1-py36_0                       --> 1.12.1-py36_blas_openblas_200 conda-forge [blas_openblas]
    scikit-learn: 0.18.1-np112py36_1                  --> 0.19.1-py36_blas_openblas_200 conda-forge [blas_openblas]
    scipy:        0.19.0-np112py36_0                  --> 0.19.1-py36_blas_openblas_202 conda-forge [blas_openblas]

Proceed ([y]/n)? 

numpy-1.12.1-p 100% |#######################################################################| Time: 0:00:09 983.90 kB/s
INFO: Initializing package repository /home/kzkt/tools/infobio/share/julia/site/v0.6
INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl
ERROR: InterruptException:
Stacktrace:
 [1] getindex at ./array.jl:207 [inlined]
 [2] Base.LibGit2.Error.GitError(::Int32) at ./libgit2/error.jl:87
 [3] macro expansion at ./libgit2/error.jl:99 [inlined]
 [4] clone(::String, ::String, ::Base.LibGit2.CloneOptions) at ./libgit2/repository.jl:276
 [5] #clone#100(::String, ::Bool, ::Ptr{Void}, ::Nullable{Base.LibGit2.AbstractCredentials}, ::Function, ::String, ::String) at ./libgit2/libgit2.jl:562
 [6] (::Base.LibGit2.#kw##clone)(::Array{Any,1}, ::Base.LibGit2.#clone, ::String, ::String) at ./<missing>:0
 [7] (::Base.Pkg.Dir.##8#10{String,String})() at ./pkg/dir.jl:55
 [8] cd(::Base.Pkg.Dir.##8#10{String,String}, ::String) at ./file.jl:70
 [9] init(::String, ::String) at ./pkg/dir.jl:53
 [10] init() at ./pkg/pkg.jl:85
INFO: Initializing package repository **PATH**TO**CONDA**ENV**REMOVED**/share/julia/site/v0.6
INFO: Cloning METADATA from https://github.com/JuliaLang/METADATA.jl

warning: parsing line table prologue at ... should have ended at ... but it ended at ...

Have been seeing a bunch of warnings when Julia errors on something (copied example below). Not entirely sure what the cause is at this time, but it looks like it is coming from LLVM.

julia> akljdsfl
warning: parsing line table prologue at 0x0000e1c8 should have ended at 0x0000e52f but it ended at 0x0000e284
warning: parsing line table prologue at 0x00003c27 should have ended at 0x00003ffc but it ended at 0x00003ce3
warning: parsing line table prologue at 0x0001cd5c should have ended at 0x0001d0f0 but it ended at 0x0001ce25
warning: parsing line table prologue at 0x000086e2 should have ended at 0x00008ae4 but it ended at 0x000087ef
warning: parsing line table prologue at 0x0000a9c0 should have ended at 0x0000ace8 but it ended at 0x0000aa7c
ERROR: UndefVarError: akljdsfl not defined