# Julia, quarto and CSV fails precompile

**URL:** <https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300>\
**Category:** General Usage\
**Created:** [March 19, 2023, 10:23am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300 "2023-03-19T10:23:03Z")\
**Posts on this page:** 17\
**Page:** 1

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 19, 2023, 10:23am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/1 "2023-03-19T10:23:03Z")

</div>

Hi All

I was experimenting with [quarto](https://quarto.org/) and ran into a strange problem with CSV. I am on the latest Julia on a M1, with all latest packages. Running Julia by itself, no problems with `using CSV` but with quarto precompile fails, with errors below. All other packages I tried work.

any idea?

Thanks, Jack

code is qmd file (for quarto)

````julia
 ---

 ---

 ```{julia}
 using Statistics;  
 ```.

```{julia}
using CSV
```.

````

and what I get is

```julia
quarto render xx.qmd

Executing 'xx.ipynb'
  Cell 1/2...Done
  Cell 2/2...ERROR:

An error occurred while executing the following cell:
------------------
using CSV
------------------

Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /Users/jack/.julia/compiled/v1.8/CSV/jl_YGglru.

Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
   @ Base ./loading.jl:1707
 [3] compilecache
   @ ./loading.jl:1651 [inlined]
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1337
 [5] _require_prelocked(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1200
 [6] macro expansion
   @ ./loading.jl:1180 [inlined]
 [7] macro expansion
   @ ./lock.jl:223 [inlined]
 [8] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1144
LoadError: Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /Users/jack/.julia/compiled/v1.8/CSV/jl_YGglru.

```

---

<div class="post-metadata">

**Author:** ![jules](https://avatars.discourse-cdn.com/v4/letter/j/41988e/32.png) [@jules](https://discourse.julialang.org/u/jules)\
**Post date:** [March 19, 2023, 10:28am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/2 "2023-03-19T10:28:30Z")

</div>

When the compile cache errors I usually just remove either only the compilation cache for just the affected package or all packages, it’s in `.julia/compiled` or so. That seems to happen rarely when I exit out of precompilation early or Julia crashes during that phase.

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 19, 2023, 10:35am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/3 "2023-03-19T10:35:23Z")

</div>

Thanks,

I did already try that and it still fails.

---

<div class="post-metadata">

**Author:** ![dmbates](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/dmbates/32/44_2.png) [@dmbates](https://discourse.julialang.org/u/dmbates)\
**Post date:** [March 19, 2023, 1:58pm UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/4 "2023-03-19T13:58:11Z")

</div>

What version of quarto and what version of Julia? Run

```julia
quarto check

```

from the shell to get the version of quarto and

```julia
julia> versioninfo()

```

to get the version of Julia.

Do you have a local `Project.toml` file? Quarto uses conversion to a Jupyter notebook, as you can see in your code snippet, where it was running code chunks of `xx.ipynb` when the error was encountered. Is `CSV` available in the local project?

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 19, 2023, 2:28pm UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/5 "2023-03-19T14:28:43Z")

</div>

Thanks

maybe the solution is to nuke `.julia`.

I have that below, but also made a new jupyter file and it gives even more errors on `using CSV`. For comparison `using Statistics` works. It seems like jupyter is using some old dependencies, and julia repl not,

I no local `Project.toml` file.

I add the Jupyter error dump below.

```julia
 quarto check

[✓] Checking Quarto installation......OK
      Version: 1.2.335
      Path: /Applications/quarto/bin

```

and in julia

```julia
using CSV
[Info: Precompiling CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]

julia> versioninfo()
Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.5.0)
  CPU: 8 × Apple M2
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
  Threads: 1 on 4 virtual cores

```

from Jupyter `using CSV`

```julia
[Info: Precompiling CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]
ERROR: LoadError: ArgumentError: Package Tables does not have OrderedCollections in its dependencies:
- You may have a partially installed environment. Try `Pkg.instantiate()`
  to ensure all packages in the environment are installed.
- Or, if you have Tables checked out for development and have
  added OrderedCollections as a dependency but haven't updated your primary
  environment's manifest file, try `Pkg.resolve()`.
- Otherwise you may need to report an issue with Tables
Stacktrace:
 [1] macro expansion
   @ ./loading.jl:1167 [inlined]
 [2] macro expansion
   @ ./lock.jl:223 [inlined]
 [3] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1144
 [4] include
   @ ./Base.jl:419 [inlined]
 [5] 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::String)
   @ Base ./loading.jl:1554
 [6] top-level scope
   @ stdin:1
in expression starting at /Users/jack/.julia/packages/Tables/AcRIE/src/Tables.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile Tables [bd369af6-aec1-5ad0-b16a-f7cc5008161c] to /Users/jack/.julia/compiled/v1.8/Tables/jl_IdeU7T.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [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:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /Users/jack/.julia/packages/CSV/b8ebJ/src/CSV.jl:1
in expression starting at stdin:1
Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /Users/jack/.julia/compiled/v1.8/CSV/jl_Kq1idG.

Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
   @ Base ./loading.jl:1707
 [3] compilecache
   @ ./loading.jl:1651 [inlined]
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1337
 [5] _require_prelocked(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1200
 [6] macro expansion
   @ ./loading.jl:1180 [inlined]
 [7] macro expansion
   @ ./lock.jl:223 [inlined]
 [8] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1144

```

in juyter but not in jula repl

```julia
Pkg.instantiate()
 Warning: The active manifest file has dependencies that were resolved with a different julia version (1.7.0-beta3). Unexpected behavior may occur.
└ @ ~/Manifest.toml:0

```

---

<div class="post-metadata">

**Author:** ![dmbates](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/dmbates/32/44_2.png) [@dmbates](https://discourse.julialang.org/u/dmbates)\
**Post date:** [March 19, 2023, 4:34pm UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/6 "2023-03-19T16:34:38Z")

</div>

I would probably create a local project and add CSV in the package prompt

```julia
(1.8) pkg> activate .
(localdir) pkg> add CSV 

```

then try rendering the notebook. The Julia package system is designed to make it easy to create and preserve a local environment for projects and it seems worthwhile using it for that.

I have, in the past, nuked my `~/.julia` directory to reset the whole system, and can understand the desire to do that. If you do choose to do that remember you will need to install IJulia to be able to use Julia code chunks in quarto.

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 20, 2023, 7:34am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/7 "2023-03-20T07:34:32Z")

</div>

Nuking `.julia` does not help. Some deeper problem with julia and jupyter that manifests itself with `using CSV`. Will try on a linux, hopefully only a bug on the M1 and not intel linux.

jupyter says

```julia
ERROR: LoadError: ArgumentError: Package Tables does not have OrderedCollections in its dependencies:
- You may have a partially installed environment.

```

REPL is fine.

---

<div class="post-metadata">

**Author:** ![nilshg](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nilshg/32/2283_2.png) [@nilshg](https://discourse.julialang.org/u/nilshg)\
**Post date:** [March 20, 2023, 8:23am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/8 "2023-03-20T08:23:14Z")

</div>

I would suspect an error related to a `Parsers` version mismatch - I recall something like this used to happen with `IJulia`, maybe Quarto also has its own `Parsers` dependency?

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 20, 2023, 8:31am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/9 "2023-03-20T08:31:32Z")

</div>

I took quarto out of the equation, now only trying jupyter. And nuked `.julia`, so would not expect a `Parsers` mismatch?

---

<div class="post-metadata">

**Author:** ![nilshg](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nilshg/32/2283_2.png) [@nilshg](https://discourse.julialang.org/u/nilshg)\
**Post date:** [March 20, 2023, 9:48am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/10 "2023-03-20T09:48:35Z")

</div>

Ah sorry I didn’t properly pay attention then.

So what you are saying is you cannot do:

```julia
julia> using IJulia

julia> notebook()

## ... Jupyter browser tab opens, start a new notebook
# In notebook cells
] activate --temp
] add CSV
using CSV

```

?

```julia

```

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 20, 2023, 10:01am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/11 "2023-03-20T10:01:30Z")

</div>

Not exactly, I did in the terminal

```julia
jupyter notebook

```

and there selected the Julia kernel and then did `using CSV` which is what fails.

When I followed your steps, I ran into another issue, in that is

```julia
julia> using IJulia
julia> notebook()
install Jupyter via Conda, y/n? [y]:

```

as jupyter is installed already (with pip and not conda) and i can call it in the terminal

---

<div class="post-metadata">

**Author:** ![nilshg](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nilshg/32/2283_2.png) [@nilshg](https://discourse.julialang.org/u/nilshg)\
**Post date:** [March 20, 2023, 10:05am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/12 "2023-03-20T10:05:01Z")

</div>

Ah right so your issues seem to come from using your own python/anaconda version rather than using the miniconda which IJulia would install. That means it’ll probably be hard for others to repro given that the issue will be specific to your setup.

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 20, 2023, 10:19am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/13 "2023-03-20T10:19:46Z")

</div>

Is that it? Julia needs to have its own python setup?

That creates its own problems. I am using quarto (which is based on jupyter), and what you say makes julia incompatible with quarto. You suggest I have to invoke jupyter inside julia, and cannot have jupyter invoke julia, which is what quarto (and jupyer books, and other jupyter utilities) need.

---

<div class="post-metadata">

**Author:** ![nilshg](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nilshg/32/2283_2.png) [@nilshg](https://discourse.julialang.org/u/nilshg)\
**Post date:** [March 20, 2023, 10:24am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/14 "2023-03-20T10:24:11Z")

</div>

No, that’s not what I’m saying. Julia doesn’t require its own python installation, but by default it does use its own miniconda so most people will have that setup installed. IJulia (and I guess other tools using python) are capable of using a user supplied python installation.

My point was merely that if there are issues with Julia interacting with your local python installation it might be hard for others to repro as they might not be able to recreate your python setup easily.

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 20, 2023, 10:45am UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/15 "2023-03-20T10:45:47Z")

</div>

Thanks, I get it now.

I will try on linux on intel and see if that works. And if not, do down the rabbit hole of older versions until it works.

And on a tangent, python and its versions and breaking updates are a pain. If I get this working, I’ll put it inside a docker and use that for the foreseeable future to process our julia with quarto.

Thanks for all the help,

best jack

---

<div class="post-metadata">

**Author:** ![dmbates](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/dmbates/32/44_2.png) [@dmbates](https://discourse.julialang.org/u/dmbates)\
**Post date:** [March 20, 2023, 12:56pm UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/16 "2023-03-20T12:56:54Z")

</div>

You can select the version of python that is to be used by quarto by setting the environment variable `QUARTO_PYTHON`. For example, if you have configured the Julia package `PyCall` to install its own miniconda then

```julia
export QUARTO_PYTHON=~/.julia/conda/3/bin/python3

```

will get you that version.

I agree that having multiple conflicting installations of Python, Conda and/or Pip on a system is annoying but it seems almost inevitable.

---

<div class="post-metadata">

**Author:** ![JackStrauss](https://avatars.discourse-cdn.com/v4/letter/j/f14d63/32.png) [@JackStrauss](https://discourse.julialang.org/u/JackStrauss)\
**Post date:** [March 20, 2023, 2:25pm UTC](https://discourse.julialang.org/t/julia-quarto-and-csv-fails-precompile/96300/17 "2023-03-20T14:25:35Z")

</div>

Of course

makes perfect sense that that way,

Yes, Having to deal with virtual environments and multiple versions is a pain we escape in R and Julia.

Thanks all for the help

Jack