GNU bug report logs - #61121
Cannot import IJulia in Julia

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Theodore Ehrenborg <theodore.ehrenborg <at> gmail.com>
Subject: bug#61121: closed (Re: bug#61121: Cannot import IJulia in Julia)
Date: Thu, 09 Feb 2023 14:54:02 +0000

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Your bug report

#61121: Cannot import IJulia in Julia

which was filed against the guix package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 61121 <at> debbugs.gnu.org.

-- 
61121: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=61121
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Efraim Flashner <efraim <at> flashner.co.il>
To: Simon Tournier <zimon.toutoune <at> gmail.com>
Cc: 61121-done <at> debbugs.gnu.org,
 Theodore Ehrenborg <theodore.ehrenborg <at> gmail.com>
Subject: Re: bug#61121: Cannot import IJulia in Julia
Date: Thu, 9 Feb 2023 16:53:01 +0200

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On Tue, Jan 31, 2023 at 12:34:16PM +0100, Simon Tournier wrote:
> 
> --8<---------------cut here---------------start------------->8---
> function __init__()
>     global artifact_dir = dirname(Sys.BINDIR)
>     global cacert = normpath(Sys.BINDIR, Base.DATAROOTDIR, "julia", "cert.pem")
> end
> --8<---------------cut here---------------end--------------->8---

I've changed this line to:

global cacert = get(ENV, \"SSL_CERT_FILE\", "\"/etc/ssl/certs/ca-certificates.crt\")

and then tested it with the example at the beginning of the bug report.

> Well, somehow turn back these tests:
> 
> --8<---------------cut here---------------start------------->8---
>              ;; julia embeds a certificate, we are not doing that
>              (substitute* "stdlib/MozillaCACerts_jll/test/runtests.jl"
>                (("@test isfile\\(MozillaCACerts_jll.cacert\\)")
>                 "@test_broken isfile(MozillaCACerts_jll.cacert)"))
>              ;; since certificate is not present some tests are failing in network option
>              (substitute* "usr/share/julia/stdlib/v1.8/NetworkOptions/test/runtests.jl"
>                (("@test isfile\\(bundled_ca_roots\\(\\)\\)")
>                 "@test_broken isfile(bundled_ca_roots())")
>                (("@test ispath\\(ca_roots_path\\(\\)\\)")
>                 "@test_broken ispath(ca_roots_path())")
>                (("@test ca_roots_path\\(\\) \\!= bundled_ca_roots\\(\\)")
>                 "@test_broken ca_roots_path() != bundled_ca_roots()"))
> --8<---------------cut here---------------end--------------->8---

I wasn't able to turn these tests back on though.

-- 
Efraim Flashner   <efraim <at> flashner.co.il>   אפרים פלשנר
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From: Theodore Ehrenborg <theodore.ehrenborg <at> gmail.com>
To: bug-guix <at> gnu.org
Subject: Cannot import IJulia in Julia
Date: Sat, 28 Jan 2023 13:45:00 +0000

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Hi Guix,

I would like to run a Jupyter notebook using Julia, so I need to install
the IJulia backend:

guix install julia
julia # Enter julia REPL
] # To go into the julia pkg REPL
add IJulia
# Now type backspace to go to julia REPL
using IJulia

This produces the error:

[ Info: Precompiling IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a]
ERROR: LoadError: InitError: SystemError: opening file
"/gnu/store/npj8z0g9nx14wl22yphqfs2c5w4qk5jk-julia-1.8.3/share/julia/cert.pem":
No such file or directory

The full error message is here: https://pastebin.com/qC8yyHXT

I saw a very similar bug on Gentoo:

Without this file (which can be a symbolic link to
`/etc/ssl/certs/ca-certificates.crt`) many Julia 1.8.3 packages, e.g.
`HTTP`, do not work.
This is what happens:

julia> import HTTP
[ Info: Precompiling HTTP [cd3eb016-35fb-5094-929b-558a96fad6f3]
ERROR: LoadError: InitError: SystemError: opening file
"/usr/share/julia/cert.pem":

(https://bugs.gentoo.org/888978)

Any help would be greatly appreciated.

Best regards,
Theodore Ehrenborg

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