bug#61121: closed (Cannot import IJulia in Julia)

[GNU bug Tracking System]

Your message dated Thu, 9 Feb 2023 16:53:01 +0200
with message-id <Y+UIzdetrRVjOdxZ@3900XT>
and subject line Re: bug#61121: Cannot import IJulia in Julia
has caused the debbugs.gnu.org bug report #61121,
regarding Cannot import IJulia in Julia
to be marked as done.

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61121: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=61121
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--- Begin Message --- Subject: Cannot import IJulia in Julia Date: Sat, 28 Jan 2023 13:45:00 +0000

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

--- End Message ---

--- Begin Message --- Subject: Re: bug#61121: Cannot import IJulia in Julia Date: Thu, 9 Feb 2023 16:53:01 +0200

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.

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Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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