# CSV.read not recognizing "select" keyword

**URL:** <https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089>\
**Category:** Data\
**Tags:** csv, ijulia\
**Created:** [June 1, 2022, 10:25pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089 "2022-06-01T22:25:42Z")\
**Posts on this page:** 12\
**Page:** 1

<div class="post-metadata">

**Author:** ![CopyOfA](https://avatars.discourse-cdn.com/v4/letter/c/858c86/32.png) [@CopyOfA](https://discourse.julialang.org/u/CopyOfA)\
**Post date:** [June 1, 2022, 10:25pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/1 "2022-06-01T22:25:42Z")

</div>

I am reading in a space-delimited file using the `CSV` library in Julia.

```julia
edgeList = CSV.read(
    joinpath(dataDirectory, "out.file"),
    types=[Int, Int],
    header=["node1", "node2"],
    skipto=3,
    select=[1,2]
)

```

This yields the following error:

```julia
MethodError: no method matching CSV.File(::String; types=DataType[Int64, Int64], header=["node1", "node2"], skipto=3, select=[1, 2])
Closest candidates are:
  CSV.File(::Any; header, normalizenames, datarow, skipto, footerskip, limit, transpose, comment, use_mmap, ignoreemptylines, missingstrings, missingstring, delim, ignorerepeated, quotechar, openquotechar, closequotechar, escapechar, dateformat, decimal, truestrings, falsestrings, type, types, typemap, categorical, pool, strict, silencewarnings, threaded, debug, parsingdebug, allowmissing) at /Users/n.jordanjameson/.julia/packages/CSV/4GOjG/src/CSV.jl:221 got unsupported keyword argument "select"

```

I am using Julia v. 1.6.2. Here is the output `versioninfo()`:

```julia
Julia Version 1.6.2
Commit 1b93d53fc4 (2021-07-14 15:36 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin18.7.0)
  CPU: Intel(R) Core(TM) i7-5650U CPU @ 2.20GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, broadwell)

```

The version of `CSV` is 0.10.4. The wiki for this version of `CSV` is here: [Reading · CSV.jl](https://csv.juliadata.org/stable/reading.html#CSV.read), and it has a `select / drop` entry.

---

<div class="post-metadata">

**Author:** ![nalimilan](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nalimilan/32/147_2.png) [@nalimilan](https://discourse.julialang.org/u/nalimilan)\
**Post date:** [June 2, 2022, 7:27am UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/2 "2022-06-02T07:27:22Z")

</div>

AFAICT you’re not using CSV.jl 0.10.4 as you think, as the path .julia/packages/CSV/4GOjG/ doesn’t match the ID used by that version, and there’s no line 222 in CSV.jl in that release: [CSV.jl/CSV.jl at v0.10.4 · JuliaData/CSV.jl · GitHub](https://github.com/JuliaData/CSV.jl/blob/v0.10.4/src/CSV.jl)

What does `]st CSV` print?

---

<div class="post-metadata">

**Author:** ![CopyOfA](https://avatars.discourse-cdn.com/v4/letter/c/858c86/32.png) [@CopyOfA](https://discourse.julialang.org/u/CopyOfA)\
**Post date:** [June 2, 2022, 1:58pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/3 "2022-06-02T13:58:35Z")

</div>

Here is the output of `]st CSV`:

```julia
      Status `~/.julia/environments/graph_env/Project.toml`
  [336ed68f] CSV v0.10.4

```

---

<div class="post-metadata">

**Author:** ![CopyOfA](https://avatars.discourse-cdn.com/v4/letter/c/858c86/32.png) [@CopyOfA](https://discourse.julialang.org/u/CopyOfA)\
**Post date:** [June 2, 2022, 2:08pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/4 "2022-06-02T14:08:11Z")

</div>

It looks like I’m encountering a new problem now, after restarting Julia. I am using a virtual environment here.

```julia
using Pkg

Pkg.activate("~/.julia/environments/graph_env/")

Pkg.status()

      Status `~/.julia/environments/graph_env/Project.toml`
  [336ed68f] CSV v0.10.4
  [a93c6f00] DataFrames v1.3.4
  [31c24e10] Distributions v0.25.62
  [38e38edf] GLM v1.8.0
  [28b8d3ca] GR v0.64.3
  [a2cc645c] GraphPlot v0.5.2
  [86223c79] Graphs v1.7.0
  [7073ff75] IJulia v1.23.3
  [093fc24a] LightGraphs v1.3.5
  [91a5bcdd] Plots v1.29.0
  [92933f4c] ProgressMeter v1.7.2
  [fc66bc1b] SNAPDatasets v0.2.0
  [ea10d353] WeakRefStrings v1.4.2
  [ade2ca70] Dates

```

The error comes from `using CSV`:

```julia
using CSV

┌ Info: Precompiling CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]
└ @ Base loading.jl:1342
ERROR: LoadError: LoadError: UndefVarError: PosLen not defined
Stacktrace:
  [1] top-level scope
    @ ~/.julia/packages/WeakRefStrings/31nkb/src/poslenstrings.jl:6
  [2] include(mod::Module, _path::String)
    @ Base ./Base.jl:386
  [3] include(x::String)
    @ WeakRefStrings ~/.julia/packages/WeakRefStrings/31nkb/src/WeakRefStrings.jl:1
  [4] top-level scope
    @ ~/.julia/packages/WeakRefStrings/31nkb/src/WeakRefStrings.jl:547
  [5] include
    @ ./Base.jl:386 [inlined]
  [6] 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:1235
  [7] top-level scope
    @ none:1
  [8] eval
    @ ./boot.jl:360 [inlined]
  [9] eval(x::Expr)
    @ Base.MainInclude ./client.jl:446
 [10] top-level scope
    @ none:1
in expression starting at /Users/n.jordanjameson/.julia/packages/WeakRefStrings/31nkb/src/poslenstrings.jl:6
in expression starting at /Users/n.jordanjameson/.julia/packages/WeakRefStrings/31nkb/src/WeakRefStrings.jl:1
ERROR: LoadError: Failed to precompile WeakRefStrings [ea10d353-3f73-51f8-a26c-33c1cb351aa5] to /Users/n.jordanjameson/.julia/compiled/v1.6/WeakRefStrings/jl_4mHO8D.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{Base.PipeEndpoint}, 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
  [7] include
    @ ./Base.jl:386 [inlined]
  [8] 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
  [9] top-level scope
    @ none:1
 [10] eval
    @ ./boot.jl:360 [inlined]
 [11] eval(x::Expr)
    @ Base.MainInclude ./client.jl:446
 [12] top-level scope
    @ none:1
in expression starting at /Users/n.jordanjameson/.julia/packages/CSV/jFiCn/src/CSV.jl:1
Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /Users/n.jordanjameson/.julia/compiled/v1.6/CSV/jl_SF4MfC.

Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IJulia.IJuliaStdio{Base.PipeEndpoint}, internal_stdout::IJulia.IJuliaStdio{Base.PipeEndpoint}, 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
 [7] eval
   @ ./boot.jl:360 [inlined]
 [8] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:1116

```

---

<div class="post-metadata">

**Author:** ![nalimilan](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nalimilan/32/147_2.png) [@nalimilan](https://discourse.julialang.org/u/nalimilan)\
**Post date:** [June 2, 2022, 4:53pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/5 "2022-06-02T16:53:53Z")

</div>

Hmm, again it seems that the printed versions of packages are not the ones that are actually used. We’ve seen this in the past (in particular related to CSV), but it’s not clear to me why. Are you running Julia in Atom maybe?

---

<div class="post-metadata">

**Author:** ![CopyOfA](https://avatars.discourse-cdn.com/v4/letter/c/858c86/32.png) [@CopyOfA](https://discourse.julialang.org/u/CopyOfA)\
**Post date:** [June 2, 2022, 5:10pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/6 "2022-06-02T17:10:10Z")

</div>

What’s odd here is that when I use `IJulia; notebook()`, I get this error, but if I use Julia from the terminal, I do not. And this happens repeatedly. I’ve exited all terminal windows, restarted terminal, restarted julia, then executed the commands:

```julia
using IJulia
notebook()

```

After the Jupyter notebook is open, I execute the code:

```julia
using Pkg
Pkg.activate("~/.julia/environments/graph_env")

using CSV

```

and get an error. However, if I only open a terminal, start Julia, and execute the same commands as above, there is no problem. Is there something with `IJulia` that makes it reach back into the base environment for packages?

---

<div class="post-metadata">

**Author:** ![nalimilan](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/nalimilan/32/147_2.png) [@nalimilan](https://discourse.julialang.org/u/nalimilan)\
**Post date:** [June 2, 2022, 9:14pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/7 "2022-06-02T21:14:48Z")

</div>

Yes I think this happens from time to time with IJulia. Maybe others will be able to tell you more.

(BTW, please mention when you cross-post to avoid having people replying twice without seeing previous messages. This one is also at [Julia CSV.read not recognizing "select" keyword - Stack Overflow](https://stackoverflow.com/questions/72468079/julia-csv-read-not-recognizing-select-keyword))

---

<div class="post-metadata">

**Author:** ![jd-foster](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jd-foster/32/35824_2.png) [@jd-foster](https://discourse.julialang.org/u/jd-foster)\
**Post date:** [June 2, 2022, 10:03pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/8 "2022-06-02T22:03:08Z")

</div>

> [@CopyOfA](#):
>
> Is there something with `IJulia` that makes it reach back into the base environment for packages?

IJulia doesn’t automatically use your currently active environment when you launch from the REPL, but the kernel that is activated in the Jupyter notebook session.

See

> [@IJulia Kernel not starting unless IJulia is installed in the global environment, ie (v1.1)](https://discourse.julialang.org/t/ijulia-kernel-not-starting-unless-ijulia-is-installed-in-the-global-environment-ie-v1-1/21172/6):
>
> If you want to run it in particular project, you can do so but you need to [install a custom kernel specification](https://github.com/JuliaLang/IJulia.jl#installing-additional-julia-kernels) that passes --project=.... when it launches julia.

I have a pull request that updates the docs as:

If an existing `Project.toml` file is not found then, by default, an IJulia notebook will try to run a Julia kernel  
with its active project set from the global or default environment (usually of the form `~/.julia/environments/v1.x`).  
If the IJulia package is not installed in that environment, then the Julia kernel selected by default will not be able to  
connect, and a **Connection failed** error will be displayed. In this case, users should install a additional  
Julia kernel that uses their chosen Julia environment.  
For example, if the desired environment is currently activated in the REPL then one possibility is to execute

```julia
IJulia.installkernel("Julia MyProjectEnv", "--project=$(Base.active_project())")

```

and subsequently select the kernel starting with `Julia MyProjectEnv` from _Kernel \> Change Kernel_ in the menu of the Jupyter notebook.

---

<div class="post-metadata">

**Author:** ![CopyOfA](https://avatars.discourse-cdn.com/v4/letter/c/858c86/32.png) [@CopyOfA](https://discourse.julialang.org/u/CopyOfA)\
**Post date:** [June 2, 2022, 10:17pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/9 "2022-06-02T22:17:48Z")

</div>

But in this case I am specifically activating the environment with `Pkg.activate("~/.Julia/environments/graph_env")`, right? You can see in the printout of `Pkg.status()` that I have `IJulia` installed in this environment as well.

---

<div class="post-metadata">

**Author:** ![jd-foster](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jd-foster/32/35824_2.png) [@jd-foster](https://discourse.julialang.org/u/jd-foster)\
**Post date:** [June 3, 2022, 3:42am UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/10 "2022-06-03T03:42:26Z")

</div>

Good observation. Maybe you can remove the duplicate packages in the environment you launch in. What is `Pkg.status()` done in Jupyter before you activate `graph_env`?

---

<div class="post-metadata">

**Author:** ![CopyOfA](https://avatars.discourse-cdn.com/v4/letter/c/858c86/32.png) [@CopyOfA](https://discourse.julialang.org/u/CopyOfA)\
**Post date:** [June 3, 2022, 10:46pm UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/11 "2022-06-03T22:46:25Z")

</div>

Just using the Julia 1.6.2 kernel:

```julia
using Pkg

Pkg.status()

      Status `~/.julia/environments/v1.6/Project.toml`
  [336ed68f] CSV v0.5.23
  [324d7699] CategoricalArrays v0.7.7
  [8be319e6] Chain v0.4.10
  [a81c6b42] Compose v0.8.2
  [a93c6f00] DataFrames v0.18.4
  [c91e804a] Gadfly v1.2.1
  [cd3eb016] HTTP v0.8.19
  [7073ff75] IJulia v1.23.3
  [43edad99] InstantiateFromURL v0.6.0
  [682c06a0] JSON v0.21.1
  [22d8b318] OAuth v0.7.1
  [91a5bcdd] Plots v1.29.0
  [ce6b1742] RDatasets v0.7.7
  [92393bbf] Twitter v0.8.1
  [f8ef4a19] VirtualEnv v1.0.0

```

And then I activate a different environment:

```julia
Pkg.activate("~/.julia/environments/graph_env/")

  Activating environment at `~/.julia/environments/graph_env/Project.toml`

Pkg.status()

      Status `~/.julia/environments/graph_env/Project.toml`
  [336ed68f] CSV v0.10.4
  [a93c6f00] DataFrames v1.3.4
  [31c24e10] Distributions v0.25.62
  [38e38edf] GLM v1.8.0
  [28b8d3ca] GR v0.64.3
  [a2cc645c] GraphPlot v0.5.2
  [86223c79] Graphs v1.7.0
  [7073ff75] IJulia v1.23.3
  [093fc24a] LightGraphs v1.3.5
  [91a5bcdd] Plots v1.29.0
  [92933f4c] ProgressMeter v1.7.2
  [fc66bc1b] SNAPDatasets v0.2.0
  [ea10d353] WeakRefStrings v1.4.2
  [ade2ca70] Dates

```

You’ll notice that the hash for the libraries that are in both the base environment and “graph\_env” are the same. I’m not sure why this is the case.

---

<div class="post-metadata">

**Author:** ![jd-foster](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jd-foster/32/35824_2.png) [@jd-foster](https://discourse.julialang.org/u/jd-foster)\
**Post date:** [June 6, 2022, 1:40am UTC](https://discourse.julialang.org/t/csv-read-not-recognizing-select-keyword/82089/12 "2022-06-06T01:40:04Z")

</div>

Ok, after some digging. This looks like a known issue:  
[https://github.com/JuliaData/CSV.jl/issues/912](https://github.com/JuliaData/CSV.jl/issues/912)

It comes down to the situation described here:  
[https://github.com/JuliaLang/julia/issues/35663](https://github.com/JuliaLang/julia/issues/35663)

I have a few recommendations to get around this. Basically, you should make sure you activate your working environment as the very first thing you do in the script, before any `using` or `import` package statements. Also, update your packages in your base environment (`v1.6`) to the latest possible versions.

Finally, if you are using the `graph_env` environment, make sure your IJulia kernel in your workbook is using it as the default:

```julia
IJulia.installkernel("Julia GraphEnv", "--project=GraphEnvProjectPath")

```

where `GraphEnvProjectPath` is the path to your project folder, and select this kernel for your workbook.  
Alternatively, launch your Jupyter notebook session in the REPL from that project environment folder ([Using IJulia · IJulia](https://julialang.github.io/IJulia.jl/dev/manual/usage/#Julia-projects));  
`julia --project=~/.julia/environments/graph_env`

Also, are you using `VirtualEnv.jl` somewhere? I’m not familiar with this package but it might mess with some of this native environment management.