I have installed cocalc image on google cloud (https://github.com/sagemathinc/cocalc-docker/blob/master/Dockerfile)
I have tried to add julia 1.4 kernel to jupyter but it failed.
I have set .julia to be here : /usr/local/share/.julia.
Config
julia bin directory : /opt/julia/bin/julia
ln -s /opt/julia/bin/julia /usr/local/bin
IJulia is installed
using Pkg ;
Pkg.add("IJulia");
etc/julia/startup.jl
ENV["JULIA_DEPOT_PATH"] = "/usr/local/share/.julia" ;
ENV["JUPYTER"] = "/usr/local/bin/jupyter";
/usr/local/share/jupyter/kernels/julia-1.4/kernel.json
{
"display_name": "Julia 1.4.0",
"argv": [
"/opt/julia/bin/julia",
"-i",
"--startup-file=yes",
"--color=yes",
"--project=#.",
"/usr/local/share/.julia/packages/IJulia/yLI42/src/kernel.jl",
"{connection_file}"
],
"language": "julia",
"env": {},
"interrupt_mode": "signal"
}
Error I get
sh-4.4$ jupyter console --kernel=julia-1.4
ERROR: LoadError: ArgumentError: Package IJulia not found in current path:
- Run `import Pkg; Pkg.add("IJulia")` to install the IJulia package.
Stacktrace:
[1] require(::Module, ::Symbol) at ./loading.jl:892
[2] include(::Module, ::String) at ./Base.jl:377
[3] exec_options(::Base.JLOptions) at ./client.jl:288
[4] _start() at ./client.jl:484
It seems that I don't understand Julia package management for projects (""--project=#." options in kernel.json).
EDIT
according to the julia Pkg Doc, the --project=#. command line tags makes Julia search for *.toml files in parent directories. But even by changing ./julia directory to the project parent directory, it does not work.
Related
This might be connected to this or this. However, none of the suggested solutions works for me.
I'm using VSCode with the Julia extension and I run everything in a Jupyter notebook. My first cell looks as follows.
using Distributions
using StatsBase
using CSV
using DataFrames
using HypothesisTests
using Plots
using GLM
using StatsPlots
Executing the cell yields to the following error.
ailed to precompile StatsPlots [f3b207a7-027a-5e70-b257-86293d7955fd] to /home/david/.julia/compiled/v1.7/StatsPlots/jl_27z7QU.
Stacktrace:
[1] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
# Base ./loading.jl:1466
[2] compilecache(pkg::Base.PkgId, path::String)
# Base ./loading.jl:1410
[3] _require(pkg::Base.PkgId)
# Base ./loading.jl:1120
[4] require(uuidkey::Base.PkgId)
# Base ./loading.jl:1013
[5] require(into::Module, mod::Symbol)
# Base ./loading.jl:997
[6] eval
# ./boot.jl:373 [inlined]
[7] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
# Base ./loading.jl:1196
[8] #invokelatest#2
# ./essentials.jl:716 [inlined]
[9] invokelatest
# ./essentials.jl:714 [inlined]
[10] (::VSCodeServer.var"#150#151"{VSCodeServer.NotebookRunCellArguments, String})()
# VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.5.11/scripts/packages/VSCodeServer/src/serve_notebook.jl:18
[11] withpath(f::VSCodeServer.var"#150#151"{VSCodeServer.NotebookRunCellArguments, String}, path::String)
# VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.5.11/scripts/packages/VSCodeServer/src/repl.jl:185
[12] notebook_runcell_request(conn::VSCodeServer.JSONRPC.JSONRPCEndpoint{Base.PipeEndpoint, Base.PipeEndpoint}, params::VSCodeServer.NotebookRunCellArguments)
# VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.5.11/scripts/packages/VSCodeServer/src/serve_notebook.jl:14
[13] dispatch_msg(x::VSCodeServer.JSONRPC.JSONRPCEndpoint{Base.PipeEndpoint, Base.PipeEndpoint}, dispatcher::VSCodeServer.JSONRPC.MsgDispatcher, msg::Dict{String, Any})
# VSCodeServer.JSONRPC ~/.vscode/extensions/julialang.language-julia-1.5.11/scripts/packages/JSONRPC/src/typed.jl:67
[14] serve_notebook(pipename::String; crashreporting_pipename::String)
# VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.5.11/scripts/packages/VSCodeServer/src/serve_notebook.jl:94
[15] top-level scope
# ~/.vscode/extensions/julialang.language-julia-1.5.11/scripts/notebook/notebook.jl:12
Next, I have opened the Julia command line and removed the StatsPlots extensions using ] rm "StatsPlots" and readded it using ] add "StatsPlots" with no success. I have tried to execute precompile in the command line by hand which yields to the following output.
(#v1.7) pkg> precompile
Precompiling project...
✗ Arpack
✗ MultivariateStats
✗ StatsPlots
0 dependencies successfully precompiled in 11 seconds (216 already precompiled)
ERROR: The following 1 direct dependency failed to precompile:
StatsPlots [f3b207a7-027a-5e70-b257-86293d7955fd]
Failed to precompile StatsPlots [f3b207a7-027a-5e70-b257-86293d7955fd] to /home/david/.julia/compiled/v1.7/StatsPlots/jl_1XjxNk.
ERROR: LoadError: InitError: could not load library "/home/david/.julia/artifacts/cdf6dc8aa6771a61c6c65a5a5c1a8d1b75f50a2f/lib/libarpack.so"
libopenblas64_.so: cannot open shared object file: No such file or directory
Stacktrace:
[1] macro expansion
# ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
[2] __init__()
# Arpack_jll ~/.julia/packages/Arpack_jll/zfgpQ/src/wrappers/x86_64-linux-gnu-libgfortran5.jl:10
[3] top-level scope (repeats 2 times)
# none:1
during initialization of module Arpack_jll
in expression starting at /home/david/.julia/packages/Arpack/pLziT/src/Arpack.jl:2
ERROR: LoadError: Failed to precompile Arpack [7d9fca2a-8960-54d3-9f78-7d1dccf2cb97] to /home/david/.julia/compiled/v1.7/Arpack/jl_fCy8AR.
Stacktrace:
[1] include(x::String)
# MultivariateStats ~/.julia/packages/MultivariateStats/zLpz8/src/MultivariateStats.jl:1
[2] top-level scope
# ~/.julia/packages/MultivariateStats/zLpz8/src/MultivariateStats.jl:113
[3] top-level scope (repeats 2 times)
# none:1
in expression starting at /home/david/.julia/packages/MultivariateStats/zLpz8/src/kpca.jl:3
in expression starting at /home/david/.julia/packages/MultivariateStats/zLpz8/src/MultivariateStats.jl:1
ERROR: LoadError: Failed to precompile MultivariateStats [6f286f6a-111f-5878-ab1e-185364afe411] to /home/david/.julia/compiled/v1.7/MultivariateStats/jl_8Rrih5.
Stacktrace:
[1] top-level scope (repeats 2 times)
# none:1
in expression starting at /home/david/.julia/packages/StatsPlots/CpWiU/src/StatsPlots.jl:1
I have tried to restart the Julia kernel, restart VSCode, and I've tried the solution suggested in the second link that I have provided, meaning removing the package and run gc.
I have also removed and readded MultivariateStats and Arpack but the above error remains.
It might be from interest that it has worked before. I run into a different error first by executing the following cell.
#df data density(:Age, group = :Treatment, title = "Distribution of ages by treatment group", xlab = "Age", ylab="Distribution", legend=:topright)
The above yielded to the following error message.
LoadError: UndefVarError: #df not defined
It might have been the case that I accidently added the outdated extension StatPlots and that might have caused the above issue. However, I've removed the old extension and added the new one.
How can I resolve the above problem?
Edit: Running Pkg.status() yields to the following output.
(#v1.7) pkg> status
Status `~/.julia/environments/v1.7/Project.toml`
[336ed68f] CSV v0.10.2
[8f4d0f93] Conda v1.6.0
[a93c6f00] DataFrames v1.3.2
[31c24e10] Distributions v0.25.48
[38e38edf] GLM v1.6.1
[a2cc645c] GraphPlot v0.5.0
[86223c79] Graphs v1.6.0
[09f84164] HypothesisTests v0.10.6
[7073ff75] IJulia v1.23.2
[91a5bcdd] Plots v1.25.8
[c3e4b0f8] Pluto v0.18.0
[7f904dfe] PlutoUI v0.7.23
[438e738f] PyCall v1.93.0
[d330b81b] PyPlot v2.10.0
[aa4a32ff] SimpleHypergraphs v0.2.0
[2913bbd2] StatsBase v0.33.14
[f3b207a7] StatsPlots v0.14.33
I was able to resolve the problem. The root of the problem was the missing library libopenblas64. This could be due to a faulty Julia installation. Here is what I have done.
First, open the Julia command line and execute the following two commands.
using Libdl
filter!(p -> occursin("blas", p), Libdl.dllist())
In my case, this yielded to the following output.
1-element Array{String,1}:
"/usr/bin/../lib/libblas.so"
I have found a similar issue in this Github issue. The correct hint is given there as well. Since I am using Manjaro (built on the Arch Linux operating system), there might have been a problem with the Julia installation package that I used.
I removed my Julia installation and installed the official binaries: julia-bin by executing the following command.
yay -S julia-bin
Open the Julia command line again and run the first two commands. This time the output is as follows.
julia> filter!(p -> occursin("blas", p), Libdl.dllist())
2-element Vector{String}:
"/usr/bin/../lib/julia/libopenblas64_.so"
"/usr/bin/../lib/julia/libblastrampoline.so"
Executing my notebook works as expected now.
JuliaPro - https://juliacomputing.com/products/juliapro/
I just get this Error with JuliaPro 1.5.2 - JupyterNote works fine -
MacBook Pro 2019 - Tried to uninstall and reinstall, but I'm not understanding why JuliaPro is giving me this error.
EDIT: Mac - Security & Privacy - Files and Folders - Atom all checked - JuliaPro-1.5.2.app - all checked
Full Disk Access - checked
Atom v0.12.23,
CSV v0.7.7,
DataFrames v0.21.8,
Glob v1.3.0,
IJulia v1.22.0,
JuliaDB v0.13.0,
Juno v0.8.4,
Pipe v1.3.0,
PkgAuthentication v0.3.0,
Weave v0.10.6,
Statistics
using Glob, CSV, Tables, DataFrames
fileDirectory = "/Users/Documents/CSV"
files = glob("*.csv", fileDirectory)
ERROR: SystemError: unable to read directory /Users/Documents/CSV: Operation not permitted
Stacktrace:
[1] readdir(::String; join::Bool, sort::Bool) at ./file.jl:780
[2] readdir at ./file.jl:775 [inlined]
[3] _glob!(::Array{String,1}, ::Glob.FilenameMatch{SubString{String}}) at /Users/.julia/packages/Glob/GOSfX/src/Glob.jl:399
[4] glob(::String, ::String) at /Users/.julia/packages/Glob/GOSfX/src/Glob.jl:367
[5] top-level scope at none:1
EDIT to Error: This shows up in Atom
Juno-julia-run
Argument to path.dirname must be a string
Object.dirname - /Applications/JuliaPro-1.5.2-1.app/Contents/MacOS/JuliaPro-Juno-1.5.2-1.app/Contents/Resources/JuliaPro-Juno-1.5.2-1/Contents/Resources/app.asar/src/electron-shims.js:9:10
- /Applications/JuliaPro-1.5.2-1.app/Contents/MacOS/JuliaPro-Juno-1.5.2-1.app/Contents/Resources/julia_atom_1.5.2-1/packages/JuliaRun-in-JuliaPro/lib/fs-utils.js:29:31
Generator.throw - null:null:null
step - /Applications/JuliaPro-1.5.2-1.app/Contents/MacOS/JuliaPro-Juno-1.5.2-1.app/Contents/Resources/julia_atom_1.5.2-1/packages/JuliaRun-in-JuliaPro/lib/fs-utils.js:41:273
Julia is not in my wheelhouse yet, but I have been handed a Julia project to run the code within.
This consists of a directory containing a main.jl, a Project.toml and a Manifest.toml.
I've read up a little on what the TOML files are for; to summarise my current understanding, they form a project or environment (not sure which, or what the real difference is).
I have installed Julia v1.3.1 at the command line by downloading the tar, decompressing and placing in my path. Typing julia at the command line opens the Julia CLI REPL as expected.
I have tried to run the code by using julia main.jl, this results in complaints about the required packages not being present, e.g.:
julia main.jl
ERROR: LoadError: ArgumentError: Package JSON not found in current path:
- Run `import Pkg; Pkg.add("JSON")` to install the JSON package.
Stacktrace:
[1] require(::Module, ::Symbol) at ./loading.jl:887
[2] include at ./boot.jl:328 [inlined]
[3] include_relative(::Module, ::String) at ./loading.jl:1105
[4] include(::Module, ::String) at ./Base.jl:31
[5] exec_options(::Base.JLOptions) at ./client.jl:287
[6] _start() at ./client.jl:460
in expression starting at /home/<user>/myproject/main.jl:3
I can follow the instructions here and load the required packages, but surely I shouldn't do this manually for every package?
As every package required is listed in the Project.toml I guess there should be some way to tell Julia to make sure the packages in the project are made available (I'm thinking something along the lines of Python's requirements file).
I have tried julia --project=main.jl, but this just results in the REPL loading again with nothing happening (not sure if any project or environment is loaded or not).
How can I tell Julia to run the script in this project while taking note of the requirements and other information in the TOML files?
Update:
Have figured out to enter ] at the REPL to enter the pkg package manager. Then I can:
(v1.3) pkg> activate .
Activating environment at `~/myproject/Project.toml`
(myproject) pkg> instantiate
(myproject) pkg>
Then leave the manager by pressing backspace.
Still not sure how to "run" everything though.
You’re very close to the solution! If the files are all in a directory dir then the command would be
julia --project=dir main.jl
You could also start an interactive session in that environment and then run the code in the file via
julia --project=dir
julia> include(“main.jl”)
Edit: If the directory is the current working directory, then you can just use --project=.
The error message Package JSON not found in current path imply that you don't have JSON installed.
You can check this by starting Julia and type using JSON
To install JSON all you have to do is writing import Pkg; Pkg.add("JSON")
See this output for example:
$ julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.5.2 (2020-09-23)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia> using JSON
ERROR: ArgumentError: Package JSON not found in current path:
- Run `import Pkg; Pkg.add("JSON")` to install the JSON package.
Stacktrace:
[1] require(::Module, ::Symbol) at ./loading.jl:893
julia> import Pkg; Pkg.add("JSON")
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
Resolving package versions...
Updating `~/.julia/environments/v1.5/Project.toml`
[682c06a0] + JSON v0.21.1
Updating `~/.julia/environments/v1.5/Manifest.toml`
[682c06a0] + JSON v0.21.1
[69de0a69] + Parsers v1.1.0
[ade2ca70] + Dates
[a63ad114] + Mmap
[de0858da] + Printf
[4ec0a83e] + Unicode
julia> using JSON
[ Info: Precompiling JSON [682c06a0-de6a-54ab-a142-c8b1cf79cde6]
julia>
I'm trying to download a file from GitHub using Julia in Jupyter Notebook:
isfile("housing.data") ||
download("https://raw.githubusercontent.com/MikeInnes/notebooks/master/housing.data",
"housing.data")
rawdata = readdlm("housing.data")'
I have Windows and Julia v1.1.1 version. I get the error message that doesn't say anything to me:
failed process: Process(`'C:\WINDOWS\System32\WindowsPowerShell\v1.0\powershell.exe' -Version 3 -NoProfile -Command "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12; (New-Object System.Net.Webclient).DownloadFile('https://raw.githubusercontent.com/MikeInnes/notebooks/master/housing.data', 'housing.data')"`, ProcessExited(3221225477)) [3221225477]
Stacktrace:
[1] error(::String, ::Base.Process, ::String, ::Int64, ::String) at .\error.jl:42
[2] pipeline_error at .\process.jl:785 [inlined]
[3] download(::String, ::String) at .\download.jl:20
[4] top-level scope at In[3]:1
I tried googling the message but it's too long to find anything, I didn't find any related topic with problems like this. What might be the reason for this error? Do I need to provide you with some other information?
Base.download relies on availability and configuration of system commands. In particular its documentation reads:
"this function relies on the availability of external tools such as curl, wget or fetch to download the file and is provided for convenience. For production use or situations in which more options are needed, please use a package that provides the desired functionality instead."
Following this advice you should do:
using Pkg
Pkg.add("HTTP")
using HTTP
HTTP.download("https://raw.githubusercontent.com/MikeInnes/notebooks/master/housing.data", "housing.data")
In this way you use pure Julia to download the file rather then various system tools and maintain the homogeneous behavior of your code across platforms.
I just install Julia and then JuliaPro for the IDE.
I can start Julia and work on it normally. However, when I open JuliaPro, I can not start Julia. I got this message after press Enter.
Do you know what happens and how to solve it ?
Press Enter to start Julia.
fatal: error thrown and no exception handler available.
InitError(mod=:BinaryProvider, error=ErrorException("No download engines found. We looked for: power
shell, C:\Windows\System32\WindowsPowerShell\v1.0\powershell, curl, wget, fetch, busybox. Install on
e and ensure it is available on the path.
"))
rec_backtrace at /home/Administrator/buildbot/worker/package_win64/build/src\stackwalk.c:94
record_backtrace at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:246
jl_throw at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:577
error at .\error.jl:33
macro expansion at .\logging.jl:318 [inlined]
#probe_platform_engines!#30 at C:\Users\julia\AppData\Local\Julia-1.0.1\share\julia\stdlib\v1.0\Bina
ryProvider\src\PlatformEngines.jl:258
unknown function (ip: 0000000012498FCE)
jl_fptr_trampoline at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:1831
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2184 [inlined]
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1537 [inlined]
jl_invoke at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:56
probe_platform_engines! at C:\Users\julia\AppData\Local\Julia-1.0.1\share\julia\stdlib\v1.0\BinaryPr
ovider\src\PlatformEngines.jl:134 [inlined]
__init__ at C:\Users\julia\AppData\Local\Julia-1.0.1\share\julia\stdlib\v1.0\BinaryProvider\src\Bina
ryProvider.jl:28
jl_apply_generic at /home/Administrator/buildbot/worker/package_win64/build/src\gf.c:2184
jl_apply at /home/Administrator/buildbot/worker/package_win64/build/src\julia.h:1537 [inlined]
jl_module_run_initializer at /home/Administrator/buildbot/worker/package_win64/build/src\toplevel.c:
90
_julia_init at /home/Administrator/buildbot/worker/package_win64/build/src/home/Administrator/buildb
ot/worker/package_win64/build/src\init.c:813
julia_init__threading at /home/Administrator/buildbot/worker/package_win64/build/src\task.c:302
wmain at /home/Administrator/buildbot/worker/package_win64/build/ui\repl.c:227
__tmainCRTStartup at /usr/src/debug/mingw64-x86_64-runtime-5.0.3-1/crt\crtexe.c:329
mainCRTStartup at /usr/src/debug/mingw64-x86_64-runtime-5.0.3-1/crt\crtexe.c:212
BaseThreadInitThunk at C:\windows\system32\kernel32.dll (unknown line)
RtlUserThreadStart at C:\windows\SYSTEM32\ntdll.dll (unknown line)
At the first time Atom installs at Julia Atom.jl at Juno.jl packages.
Start a Julia console (outside of Atom), go to package manager by pressing ] and type:
(v1.0) pkg> add Juno
(v1.0) pkg> add Atom
Just in case check if they precompile:
julia> using Juno
julia> using Atom
Once installed, go to Atom options by pressing Ctrl+,. Now select Packages and for julia-client click settings - in the settings Julia Path enter the full path for your Julia executable (the same one that has Juno and Atom installed).
Now Julia has good chance to work.
If it does not try to delete the .atom folder (it can be found at JuliaPro-1.0.1.1/.atom or at YOUR_HOME_DIRECTORY/.atom). Sometimes Atom package updates cause Atom Juno to stop working properly and this is the only good option.
Let me know if that helped.