I want to add cis library which has api in python.
using CondaPkg; CondaPkg.add("cis")
@abraemer
I havenβt used CondaPkg.jl so I donβt know what this error means.
However I moved the topic from Tooling to General Usage which I feel is more appropriate so you are more likely to get help from someone with more experience in Python things.
Can you show more of the output at the bottom?
CondaPkg Found dependencies: /tmp/jl_RMuNbM/CondaPkg.toml
CondaPkg Found dependencies: /home/raman/.julia/packages/PythonCall/S5MOg/CondaPkg.toml
CondaPkg Resolving changes
+ cis
+ libstdcxx-ng
+ python
CondaPkg Creating environment
β /home/raman/.julia/artifacts/7973f2c7725e2d0eef7a95159454c4145f0945a2/bin/micromamba
β -r /home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root
β create
β -y
β -p /tmp/jl_RMuNbM/.CondaPkg/env
β --override-channels
β --no-channel-priority
β cis[version='*']
β libstdcxx-ng[version='>=3.4,<13.0']
β python[version='>=3.8,<4',channel='conda-forge',build='*cpython*']
β -c conda-forge
Transaction
Prefix: /tmp/jl_RMuNbM/.CondaPkg/env
Updating specs:
- cis=*
- libstdcxx-ng[version='>=3.4,<13.0']
- conda-forge::python[version='>=3.8,<4',build=*cpython*]
Package Version Build Channel Size
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Install:
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Summary:
Install: 197 packages
Total download: 0 B
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Transaction starting
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Linking libgcrypt-1.10.3-hd590300_0
Linking libsndfile-1.2.2-hc60ed4a_1
Linking libxkbcommon-1.7.0-h662e7e4_0
Linking libcblas-3.9.0-22_linux64_openblas
Linking liblapack-3.9.0-22_linux64_openblas
Linking hdf5-1.14.3-nompi_hdf9ad27_105
Linking proj-9.4.0-hb784bbd_2
Linking libsystemd0-255-h3516f8a_1
Linking libnetcdf-4.9.2-nompi_h135f659_114
Linking pulseaudio-client-17.0-hb77b528_0
Linking tzdata-2024a-h0c530f3_0
Linking font-ttf-dejavu-sans-mono-2.37-hab24e00_0
Linking font-ttf-inconsolata-3.000-h77eed37_0
Linking font-ttf-source-code-pro-2.038-h77eed37_0
Linking font-ttf-ubuntu-0.83-h77eed37_2
Linking fonts-conda-forge-1-0
Linking fonts-conda-ecosystem-1-0
Linking python-3.11.9-hb806964_0_cpython
Linking cairo-1.18.0-h3faef2a_0
Linking harfbuzz-8.5.0-hfac3d4d_0
Linking wheel-0.43.0-pyhd8ed1ab_1
Linking setuptools-70.0.0-pyhd8ed1ab_0
critical libmamba filesystem error: cannot copy: Input/output error [/home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/command/sdist.py] [/tmp/jl_RMuNbM/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py]
Your problem is on this line. Drill into that.
How to solve that problem? I have two version of python installed on my PC.
I have no idea. Why is there a file system error? Is your disk full?
Does /home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/command/sdist.py
exist? Can you access it?
Does /tmp/jl_RMuNbM/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py
exist? Can you copy a file there?
@mkitti My Disk is not full. Yes, these file exists. Which file should i copy to /tmp⦠? May be it is not copying due to same name file already exists in /tmp.
Is there any plan to have api of cis library[5. CIS as a Python library (API) β Community Intercomparison Suite 1.6.0 (Stable) documentation] in Julia? Please help me how i can overcome my error.
CondaPkg Found dependencies: /home/raman/.julia/environments/v1.10/CondaPkg.toml
CondaPkg Found dependencies: /home/raman/.julia/packages/PythonCall/S5MOg/CondaPkg.toml
CondaPkg Resolving changes
+ libstdcxx-ng
+ python
CondaPkg Installing packages
β /home/raman/.julia/artifacts/7973f2c7725e2d0eef7a95159454c4145f0945a2/bin/micromamba
β -r /home/raman/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root
β install
β -y
β -p /home/raman/.julia/environments/v1.10/.CondaPkg/env
β --override-channels
β --no-channel-priority
β cis[version='*']
β libstdcxx-ng[version='>=3.4,<13.0']
β python[version='>=3.8,<4',channel='conda-forge',build='*cpython*']
β -c conda-forge
conda-forge/noarch 15.0MB @ 396.7kB/s 37.9s
conda-forge/linux-64 35.3MB @ 702.2kB/s 50.5s
Transaction
Prefix: /home/raman/.julia/environments/v1.10/.CondaPkg/env
Updating specs:
- cis=*
- libstdcxx-ng[version='>=3.4,<13.0']
- conda-forge::python[version='>=3.8,<4',build=*cpython*]
Package Version Build Channel Size
βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
Reinstall:
βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
o python 3.11.9 hb806964_0_cpython conda-forge Cached
Downgrade:
βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
- libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge Cached
+ libstdcxx-ng 12.3.0 hc0a3c3a_7 conda-forge Cached
Summary:
Reinstall: 1 packages
Downgrade: 1 packages
Total download: 0 B
βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
Transaction starting
Changing libstdcxx-ng-13.2.0-hc0a3c3a_7 ==> libstdcxx-ng-12.3.0-hc0a3c3a_7
Reinstalling python-3.11.9-hb806964_0_cpython
Transaction finished
To activate this environment, use:
micromamba activate /home/raman/.julia/environments/v1.10/.CondaPkg/env
Or to execute a single command in this environment, use:
micromamba run -p /home/raman/.julia/environments/v1.10/.CondaPkg/env mycommand
There is no error in what you posted. This is just the Python packager manager installing the library.
This is error. See post 4.
Linking wheel-0.43.0-pyhd8ed1ab_1
Linking setuptools-70.0.0-pyhd8ed1ab_0
critical libmamba filesystem error: cannot copy: Input/output error [/home/raman/y/pkgs/setuptools-70.0.0-pyhd8ed1ab_0/site-packages/setuptools/_distutils/dist.py] [/tmp/jl_KAmyfx/.CondaPkg/env/lib/python3.11/site-packages/setuptools/_distutils/dist.py]
I tried on Ubuntu Linux using Julia 1.10.4:
mkdir tmp
cd tmp
julia --project="."
and then in Julia:
using CondaPkg
CondaPkg.add("cis")
I get some warnings, otherwise it works fine.
julia> using CondaPkg
β Package CondaPkg not found, but a package named CondaPkg is available from a
β registry.
β Install package?
β (tmp) pkg> add CondaPkg
β (y/n/o) [y]:
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Installed MicroMamba βββββ v0.1.14
Installed micromamba_jll β v1.5.8+0
Installed CondaPkg βββββββ v0.2.22
Installed Pidfile ββββββββ v1.3.0
Installed JSON3 ββββββββββ v1.14.0
Updating `~/repos/tmp/Project.toml`
[992eb4ea] + CondaPkg v0.2.22
Updating `~/repos/tmp/Manifest.toml`
[992eb4ea] + CondaPkg v0.2.22
[692b3bcd] + JLLWrappers v1.5.0
[0f8b85d8] + JSON3 v1.14.0
[0b3b1443] + MicroMamba v0.1.14
[69de0a69] + Parsers v2.8.1
[fa939f87] + Pidfile v1.3.0
[aea7be01] + PrecompileTools v1.2.1
[21216c6a] + Preferences v1.4.3
[6c6a2e73] + Scratch v1.2.1
[856f2bd8] + StructTypes v1.10.0
[f8abcde7] + micromamba_jll v1.5.8+0
[0dad84c5] + ArgTools v1.1.1
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL v0.6.4
[76f85450] + LibGit2
[8f399da3] + Libdl
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.10.0
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[deac9b47] + LibCURL_jll v8.4.0+0
[e37daf67] + LibGit2_jll v1.6.4+0
[29816b5a] + LibSSH2_jll v1.11.0+1
[c8ffd9c3] + MbedTLS_jll v2.28.2+1
[14a3606d] + MozillaCACerts_jll v2023.1.10
[83775a58] + Zlib_jll v1.2.13+1
[8e850ede] + nghttp2_jll v1.52.0+1
[3f19e933] + p7zip_jll v17.4.0+2
Precompiling project...
5 dependencies successfully precompiled in 35 seconds. 9 already precompiled.
1 dependency had output during precompilation:
β micromamba_jll
β Downloading artifact: micromamba
β
β [pid 6296] waiting for IO to finish:
β Handle type uv_handle_t->data
β timer 0x1d33860->0x7f1837ba9d20
β This means that a package has started a background task or event source that has not finished running. For precompilation to complete successfully, the event source needs to be closed explicitly. See the developer documentation on fixing precompilation hangs for more help.
β
β [pid 6296] waiting for IO to finish:
β Handle type uv_handle_t->data
β timer 0x1d33860->0x7f1837ba9d20
β This means that a package has started a background task or event source that has not finished running. For precompilation to complete successfully, the event source needs to be closed explicitly. See the developer documentation on fixing precompilation hangs for more help.
β
I think these warnings can be ignored.
What is your output of:
versioninfo()
?
julia> versioninfo()
Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 Γ Intel(R) Core(TM) i3-4005U CPU @ 1.70GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, haswell)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Can you install it if you use micromamba directly?
ο ~ ξ° "${SHELL}" <(curl -L micro.mamba.pm/install.sh) ξ² β ξ² 3m 36s ο
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
100 3070 100 3070 0 0 1619 0 0:00:01 0:00:01 --:--:-- 187k
Micromamba binary folder? [~/.local/bin]
Init shell (zsh)? [Y/n]
Configure conda-forge? [Y/n]
Prefix location? [~/micromamba]
Modifying RC file "/home/raman/.zshrc"
Generating config for root prefix "/home/raman/micromamba"
Setting mamba executable to: "/home/raman/.local/bin/micromamba"
Adding (or replacing) the following in your "/home/raman/.zshrc" file
# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba init' !!
export MAMBA_EXE='/home/raman/.local/bin/micromamba';
export MAMBA_ROOT_PREFIX='/home/raman/micromamba';
__mamba_setup="$("$MAMBA_EXE" shell hook --shell zsh --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__mamba_setup"
else
alias micromamba="$MAMBA_EXE" # Fallback on help from mamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<
Please restart your shell to activate micromamba or run the following:
source ~/.bashrc (or ~/.zshrc, ~/.xonshrc, ~/.config/fish/config.fish, ...)
ο ξ° ο ~ ξ° ξ² β ξ² 2m 5s ο
See also
ο ξ° ο ~ ξ° micromamba install CondaPkg ξ² β
info libmamba ****************** Backtrace Start ******************
debug libmamba Loading configuration
trace libmamba Compute configurable 'create_base'
trace libmamba Compute configurable 'no_env'
trace libmamba Compute configurable 'no_rc'
trace libmamba Compute configurable 'rc_files'
trace libmamba Compute configurable 'root_prefix'
trace libmamba Get RC files configuration from locations up to HomeDir
trace libmamba Configuration not found at '/home/raman/.mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/.mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/.mambarc'
trace libmamba Configuration found at '/home/raman/.condarc'
trace libmamba Configuration not found at '/home/raman/.conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.conda/condarc'
trace libmamba Configuration not found at '/home/raman/.conda/.condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/.condarc'
trace libmamba Configuration not found at '/home/raman/y/.mambarc'
trace libmamba Configuration not found at '/home/raman/y/condarc.d'
trace libmamba Configuration not found at '/home/raman/y/condarc'
trace libmamba Configuration not found at '/home/raman/y/.condarc'
trace libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace libmamba Configuration not found at '/var/lib/conda/condarc'
trace libmamba Configuration not found at '/var/lib/conda/.condarc'
trace libmamba Configuration not found at '/etc/conda/.mambarc'
trace libmamba Configuration not found at '/etc/conda/condarc.d/'
trace libmamba Configuration not found at '/etc/conda/condarc'
trace libmamba Configuration not found at '/etc/conda/.condarc'
trace libmamba Update configurable 'no_env'
trace libmamba Compute configurable 'envs_dirs'
trace libmamba Compute configurable 'file_specs'
trace libmamba Compute configurable 'spec_file_env_name'
trace libmamba Compute configurable 'env_name'
trace libmamba Compute configurable 'use_target_prefix_fallback'
trace libmamba Compute configurable 'target_prefix'
trace libmamba Get RC files configuration from locations up to TargetPrefix
trace libmamba Configuration not found at '/home/raman/.mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.mamba/.mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/mambarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/.mambarc'
trace libmamba Configuration found at '/home/raman/.condarc'
trace libmamba Configuration not found at '/home/raman/.conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.conda/condarc'
trace libmamba Configuration not found at '/home/raman/.conda/.condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc.d'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/condarc'
trace libmamba Configuration not found at '/home/raman/.config/mamba/../conda/.condarc'
trace libmamba Configuration not found at '/home/raman/y/.mambarc'
trace libmamba Configuration not found at '/home/raman/y/condarc.d'
trace libmamba Configuration not found at '/home/raman/y/condarc'
trace libmamba Configuration not found at '/home/raman/y/.condarc'
trace libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace libmamba Configuration not found at '/var/lib/conda/condarc'
trace libmamba Configuration not found at '/var/lib/conda/.condarc'
trace libmamba Configuration not found at '/etc/conda/.mambarc'
trace libmamba Configuration not found at '/etc/conda/condarc.d/'
trace libmamba Configuration not found at '/etc/conda/condarc'
trace libmamba Configuration not found at '/etc/conda/.condarc'
trace libmamba Update configurable 'no_env'
trace libmamba Compute configurable 'relocate_prefix'
trace libmamba Compute configurable 'target_prefix_checks'
error libmamba No target prefix specified
critical libmamba Aborting.
info libmamba ****************** Backtrace End ********************
What I do sometimes to is to delete the .julia folder and start again. But think twice before doing that, better rename it. But it helps to have a clean starting point.
@mkitti The next question I have is: Does CondaPkg use PyCall or PythonCall? These two are normally not compatible (unless you apply advanced steps).
You mean i should delete Julia and reinstall it. Ok, I have no problem in doing that but tell me how to do that. I have installed it using Juliaup.
cd ~
mv .julia .julia.bak
Should i install now using Juliaup or something else? I think Juliaup would be better as i will be able to upgrade the in future.
So what should i do Juliaup or Julia? Will not Juliaup fine in my case?
If I do that on my machine and then run
julia
in the terminal Julia gets re-installed automatically. Because juliaup
lives in a different directory:
ufechner@framework:~$ which julia
/home/ufechner/.juliaup/bin/julia