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conda-forge / julia-feedstock

A conda-smithy repository for julia.
BSD 3-Clause "New" or "Revised" License
23 stars 32 forks source link

Failling to install Julia #83

Closed clementviolet closed 3 years ago

clementviolet commented 4 years ago

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 ```
ponomarevsy commented 4 years ago

I am having the same problem with julia and blas_openblash as @clementviolet. Any solutions?

ponomarevsy commented 4 years ago

As it turns out, if you just do "conda install -c conda-forge julia", as this page suggests, https://anaconda.org/conda-forge/julia, it will try installing old julia v1.0.3 instead of the v1.1.1:

julia              conda-forge/linux-64::julia-1.0.3-blas_openblash12d65f3_2

This seems to have worked for me:

conda install -c conda-forge julia=1.1.1
clementviolet commented 4 years ago

Hi! thanks for your help @ponomarevsy. I gonna try your solution later, I don't have time to dig into it right now.

KaparaNewbie commented 4 years ago

Thanks @ponomarevsy, it worked for me as well.

0xAlexS commented 4 years ago

Just wanted to leave a message here to confirm that the solution by @ponomarevsy works on my end as well, and for anyone wondering, it looks like the version of the julia conda package is still at 1.1.1, so this solution is still valid for installing the latest version of the conda package. Here is a link to the conda package web-page if anyone should need it in the future:

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