From debbugs-submit-bounces@debbugs.gnu.org Sat Jan 28 08:45:59 2023 Received: (at submit) by debbugs.gnu.org; 28 Jan 2023 13:45:59 +0000 Received: from localhost ([127.0.0.1]:39899 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLlWp-0007hI-2l for submit@debbugs.gnu.org; Sat, 28 Jan 2023 08:45:59 -0500 Received: from lists.gnu.org ([209.51.188.17]:60264) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLlWk-0007h6-0s for submit@debbugs.gnu.org; Sat, 28 Jan 2023 08:45:57 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pLlWj-0007ay-OS for bug-guix@gnu.org; Sat, 28 Jan 2023 08:45:53 -0500 Received: from mail-yw1-x1133.google.com ([2607:f8b0:4864:20::1133]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pLlWh-0005fp-Cb for bug-guix@gnu.org; Sat, 28 Jan 2023 08:45:53 -0500 Received: by mail-yw1-x1133.google.com with SMTP id 00721157ae682-4b718cab0e4so102908757b3.9 for ; Sat, 28 Jan 2023 05:45:44 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=to:subject:message-id:date:from:mime-version:from:to:cc:subject :date:message-id:reply-to; bh=ZTSouBLFQCvmFilvCJdmqnQX1OF3j0Btv+g/x7gD2kw=; b=bq1/yGAGpOIy7X4OJCjUsS+yHUp57G7YuQ1QE7i9i/9LzEQ61bzkGKxz8T2XcEOnuI vLKcthFR5PMfMSlxctgvcvZblO1Bl1EeT4QN+4ezBOmwthVcHaswfQASLMipsmHdVTvr 51LBD9W5n2slU1jnTskKjFeeDTVhVrO1N71hweJvB5Ce0D5TLhGAqxANZnq2evaorErQ J8Q3Emdr14XRXkVmjFNWeOQjMzoUJxOBuPPq/MdG2mP1BfxS6QB/scNGwbecqIxZcW2w aLm7a7F2kv7ZQRfD1oxsCgIbPy+PvtgHYAim/3xW4rfr6MKx+UmBGWVZnRNFKcRsKjhG xUIQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=to:subject:message-id:date:from:mime-version:x-gm-message-state :from:to:cc:subject:date:message-id:reply-to; bh=ZTSouBLFQCvmFilvCJdmqnQX1OF3j0Btv+g/x7gD2kw=; b=AfpRNR10UBOmoReMZOUAmvegH3RRq/Ih4a7QSSa5pnOtIWyPJUSrYFX7tZ8vJ1z2PW qzOsiR+9CkbZZsXQSRbI9FORqLFRbI+ytu8e3B+f+Jl66NBfSoTn9voP5Qcjn2rl/tHk bg+9s0DrmyOFa23Bv7EMxVBAHhvYAMaFA7OwuVI6ZQapoXUVXv3R/oEhtKb2HgACX49O TmFxWzVl72DadEr4SXq3dUe4ZS4La0X508jgEohQyoV7dtNC6eFnSZt9h3ufMVUlSWt9 DdxNEf9z6mndUKhcj8alpMIX63tJdYiwDEdLmTzjxSx3aVqMTSnxLXM9zskYACJJank6 YDOg== X-Gm-Message-State: AO0yUKW1jJZUru+ZR60jxtCuVI56FXxhTMqsaRwDgrqPr6JyTU398Paa wb4f1vY4r7BmUHQAIqR0RZj0KBT4DJleZZ4rMFhh24OaOq4= X-Google-Smtp-Source: AK7set8FEVg6mejZcXHmwWzhWSYdqZ0HHpadK7JSey0K4JQZgrEvHfkYlnAwEWv+OXkrp5gM1l5dMtMZrKcxb8ki/Cc= X-Received: by 2002:a81:620b:0:b0:506:4b55:5a39 with SMTP id w11-20020a81620b000000b005064b555a39mr2244096ywb.89.1674913543582; Sat, 28 Jan 2023 05:45:43 -0800 (PST) MIME-Version: 1.0 From: Theodore Ehrenborg Date: Sat, 28 Jan 2023 13:45:00 +0000 Message-ID: Subject: Cannot import IJulia in Julia To: bug-guix@gnu.org Content-Type: multipart/alternative; boundary="000000000000cb79fd05f35332e8" Received-SPF: pass client-ip=2607:f8b0:4864:20::1133; envelope-from=theodore.ehrenborg@gmail.com; helo=mail-yw1-x1133.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) --000000000000cb79fd05f35332e8 Content-Type: text/plain; charset="UTF-8" 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 --000000000000cb79fd05f35332e8 Content-Type: text/html; charset="UTF-8"

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

--000000000000cb79fd05f35332e8-- From debbugs-submit-bounces@debbugs.gnu.org Mon Jan 30 07:47:50 2023 Received: (at 61121) by debbugs.gnu.org; 30 Jan 2023 12:47:50 +0000 Received: from localhost ([127.0.0.1]:46595 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pMTZe-00010M-3Z for submit@debbugs.gnu.org; Mon, 30 Jan 2023 07:47:50 -0500 Received: from mail-wm1-f51.google.com ([209.85.128.51]:39928) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pMTZc-0000zP-Pf for 61121@debbugs.gnu.org; Mon, 30 Jan 2023 07:47:49 -0500 Received: by mail-wm1-f51.google.com with SMTP id hn2-20020a05600ca38200b003dc5cb96d46so970173wmb.4 for <61121@debbugs.gnu.org>; Mon, 30 Jan 2023 04:47:48 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:from:to:cc:subject:date:message-id :reply-to; bh=i2uC8ZGl8gPwCoFT3AGb1GTj4v1l6nfqObR0jpZQlzo=; b=Wrx+3U3KSsblQWd27b02WAhLWJlO59kS6Ct/zi1i2ky1opkc7eqYMtRLVFNlGRwDRi wc/zxzqK69rePKBdHiRZcxPy2w1hYsOIb744AAiE8a3b1NxnuE8lmWN9t0Qpf+o94f/r W4RYnqyoKABqd/BnKnfe3IyrO5z+jNFFsrlAPjQpJoBL7MN01uK65TWCYcntEGnMuMFS MFM3GPTPDz2umPPXyu6kWoZSOQHO+gtVg9SOgYfqTbqE+broe0pQOY8+vNLCoV4mGXY4 CUvFCjy3iSXs8XyCT+HY+43UkMRoYSPfPrAzoZd5DSRGh96didZGS2asJVVHTb3yN4C8 TE1w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=i2uC8ZGl8gPwCoFT3AGb1GTj4v1l6nfqObR0jpZQlzo=; b=YRk6+LjtXIehMnMowG5lAsZCbv+hyK7NcBaUjiBNSblCGRj7PddRytjk4AV0AZJNKc Lb5ernUoh7RRNzayDgantFQ1CtW+RnzkXrkSf6m7d/o4l5Jzw12Z9AxzFh4raf7oBSjG V4L2Okxb2kGqntRayAfGKEXYdq94MHfdIUIko5AHpvLiRkWsyA67EotCWwb/qiJsnyXb WmDB3NbWZa7tIlG8KNgbTwAimnK32cwxYd6lKR5FcldjVvXBntpSDgwyKc3NJrLWWJaR S/FksGPgxJdnarh51AT5DP7sejLJp/HjigwlDl0SIvSX9eh+NTzc8dVOJUk8iw/xy6y/ WRGQ== X-Gm-Message-State: AO0yUKWtmc2LDyUwH5PTAw2ZDZcNLnRwuCFv3lyd6TBIS490+udqjb+O 58s9vaCgOJQqL4+4jOGqE60= X-Google-Smtp-Source: AK7set9YuEEkGg/LC25FqB8nYzo3qW+K6YLHFHBg0x6iMyEhtt5vbyMtZVQFo+M6WEaSiqvj/5TABw== X-Received: by 2002:a05:600c:1e02:b0:3dc:4234:fe89 with SMTP id ay2-20020a05600c1e0200b003dc4234fe89mr2502082wmb.2.1675082863249; Mon, 30 Jan 2023 04:47:43 -0800 (PST) Received: from pfiuh07 ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id a11-20020a5d4d4b000000b00289bdda07b7sm11661857wru.92.2023.01.30.04.47.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 30 Jan 2023 04:47:42 -0800 (PST) From: Simon Tournier To: Theodore Ehrenborg , 61121@debbugs.gnu.org Subject: Re: bug#61121: Cannot import IJulia in Julia In-Reply-To: References: Date: Mon, 30 Jan 2023 13:27:50 +0100 Message-ID: <87bkmgky0p.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 61121 Cc: Efraim Flashner X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, I confirm this bug. On sam., 28 janv. 2023 at 13:45, Theodore Ehrenborg wrote: > [ 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 [...] > I saw a very similar bug on Gentoo: [...] > (https://bugs.gentoo.org/888978) Well, that=E2=80=99s because Julia upstream does not take care about packag= ers; as explicitly mentioned in this comment: https://github.com/JuliaLang/MbedTLS.jl/pull/261#issuecomment-1346886879 The Guixer Cayetano Santos fixed upstream the issue for one package. But as you are noticing it is not done for all. I do not know what is the best solution because the issue is coming from Julia itself. Efraim, any suggestion? Cheers, simon From debbugs-submit-bounces@debbugs.gnu.org Mon Jan 30 16:56:17 2023 Received: (at 61121) by debbugs.gnu.org; 30 Jan 2023 21:56:17 +0000 Received: from localhost ([127.0.0.1]:50789 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pMc8O-0008J9-OJ for submit@debbugs.gnu.org; Mon, 30 Jan 2023 16:56:17 -0500 Received: from mail-yb1-f175.google.com ([209.85.219.175]:41589) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pMc8N-0008Ix-70 for 61121@debbugs.gnu.org; Mon, 30 Jan 2023 16:56:15 -0500 Received: by mail-yb1-f175.google.com with SMTP id h5so15847864ybj.8 for <61121@debbugs.gnu.org>; Mon, 30 Jan 2023 13:56:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:from:to:cc:subject:date:message-id:reply-to; bh=EuNfeA7P0JXRKMIWXaERqNv9GgexUcx0GeEQKJWj2w8=; b=EYSnv+rYAmMUVOqyJe94S4L0gflSYiuDNJJPCWECQTc0g6ccRNqTkXe0W9L7fWFsgJ HGbU04wKTogp2Pzy5xLinSK7pKYxPBi/gI9i4LLlRlXQevRON9QwQoGrNgHsev411P4R Iy0r0Te58AJdRQgec4l71ZfGGVPPbT0h4KJhesm13CA+JcSLA9OxA5fF0DVW9w2etjmH SSSyAmnuNIo/22LQv1VGhPAePjx58hTI8Jb4y3QmAfbv1N1Zf3aMKi2zYry2l5jdsQGQ OqHC5F49KsUPRVmEBpzwjRf2usxvvMue8aMGTFDdpK75gVW3rm9NELqEwg6eKtUuhiSD Cg+Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=EuNfeA7P0JXRKMIWXaERqNv9GgexUcx0GeEQKJWj2w8=; b=L4RlQ+/7wJ+IPw24g3CYPaeNs0YkJo0MciBzf+ktm+uTf0K+51H6uF3E9sBMNTrLYn SWTTPpNtA114hTnLdhblNOaMjRUjt9wJWMnPSFpJ/UMFQ22InyoMz3v5phKPUFx1Dllq ngh9iQTraOPOHHnD8pkZwSU9bYH9poA7al+XprWHAETedJJAv6HHZ2gBzauGBSzgRax8 Z9kmBJ0GIVOYmzCPb7Eaf1Jsb/hRb3z3kJyexeU/H3OQupStx2jbYEWbL3ncPckYdC6T yluJwaM7gbWDaZ67j55TM1uSfuNxjDt+oLkWU2NJyviESOQgHL7HMX/OYSLlQIwNqM7C IxXQ== X-Gm-Message-State: AO0yUKWFDc22KNqbr7Jg11sMAppRktoJk3hERgMf8WhhIC6iziSyzuks 2v0ZBPIan8jseZ5eRX4XBsbv7VWQCjEIeweDSWI= X-Google-Smtp-Source: AK7set+ICR/jDhfoVMmx2tJxxXTKYvvGWEgog5NphH8/4UiwxPJUq8ANs5aqtTHaqBGACNoDXfKnoFcMx6X4miYbZRU= X-Received: by 2002:a25:9208:0:b0:80b:db23:b8a6 with SMTP id b8-20020a259208000000b0080bdb23b8a6mr2054243ybo.625.1675115769307; Mon, 30 Jan 2023 13:56:09 -0800 (PST) MIME-Version: 1.0 References: <87bkmgky0p.fsf@gmail.com> In-Reply-To: <87bkmgky0p.fsf@gmail.com> From: Theodore Ehrenborg Date: Mon, 30 Jan 2023 21:55:32 +0000 Message-ID: Subject: Re: bug#61121: Cannot import IJulia in Julia To: Simon Tournier Content-Type: multipart/alternative; boundary="000000000000632ca905f382488a" X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 61121 Cc: 61121@debbugs.gnu.org, Efraim Flashner X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --000000000000632ca905f382488a Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi, Thanks for getting back with me. Gentoo appears to have fixed this bug by linking julia/cert.pem to the system's ca-certificates.crt. https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3D26b59330b5222996defa= 4536237e62404bf21168 Is there a way I could rebuild my own slightly modified Julia with a link like that? I understand that there's probably a good reason that Guix's Julia doesn't by default have cert.pem, but I would be pleased with a hacky custom solution if it made Jupyter notebooks work. Thanks, Theodore Den m=C3=A5n 30 jan. 2023 kl 12:47 skrev Simon Tournier : > Hi, > > I confirm this bug. > > On sam., 28 janv. 2023 at 13:45, Theodore Ehrenborg < > theodore.ehrenborg@gmail.com> wrote: > > > [ 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 > > [...] > > > I saw a very similar bug on Gentoo: > > [...] > > > (https://bugs.gentoo.org/888978) > > Well, that=E2=80=99s because Julia upstream does not take care about pack= agers; > as explicitly mentioned in this comment: > > > https://github.com/JuliaLang/MbedTLS.jl/pull/261#issuecomment-1346886879 > > The Guixer Cayetano Santos fixed upstream the issue for one package. > But as you are noticing it is not done for all. > > I do not know what is the best solution because the issue is coming from > Julia itself. > > Efraim, any suggestion? > > Cheers, > simon > --000000000000632ca905f382488a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

Thanks for getting back = with me.

Gentoo appears to have fixed this bug by = linking julia/cert.pem to the system's ca-certificates.crt. https://gitweb.gentoo.org/repo/gentoo.git/commit/?id= =3D26b59330b5222996defa4536237e62404bf21168

Is there a way I could rebuild my own slightly modified Julia with a link= like that?

I understand that there's pro= bably a good reason that Guix's Julia doesn't by default have cert.= pem, but I would be pleased with a hacky custom solution if it made Jupyter= notebooks work.

Thanks,
Theodore

Den m=C3=A5n 30 jan. 2023 kl 12:47 skrev Simon Tournier <zimon.toutoune@gmail.com>:
=
Hi,

I confirm this bug.

On sam., 28 janv. 2023 at 13:45, Theodore Ehrenborg <theodore.ehrenborg@gmail.com= > wrote:

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

[...]

> I saw a very similar bug on Gentoo:

[...]

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

Well, that=E2=80=99s because Julia upstream does not take care about packag= ers;
as explicitly mentioned in this comment:

=C2=A0 =C2=A0 https://github= .com/JuliaLang/MbedTLS.jl/pull/261#issuecomment-1346886879

The Guixer Cayetano Santos fixed upstream the issue for one package.
But as you are noticing it is not done for all.

I do not know what is the best solution because the issue is coming from Julia itself.

Efraim, any suggestion?

Cheers,
simon
--000000000000632ca905f382488a-- From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 31 06:36:52 2023 Received: (at 61121) by debbugs.gnu.org; 31 Jan 2023 11:36:52 +0000 Received: from localhost ([127.0.0.1]:51735 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pMowW-0005Jc-9R for submit@debbugs.gnu.org; Tue, 31 Jan 2023 06:36:52 -0500 Received: from mail-wr1-f49.google.com ([209.85.221.49]:34654) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pMow7-0005Ia-C4 for 61121@debbugs.gnu.org; Tue, 31 Jan 2023 06:36:27 -0500 Received: by mail-wr1-f49.google.com with SMTP id t18so13934956wro.1 for <61121@debbugs.gnu.org>; Tue, 31 Jan 2023 03:36:27 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:from:to:cc:subject:date:message-id :reply-to; bh=73nE1OGN3cX8ujLhtyZhE/AevLnmpiTTMXVsEBTy/BM=; b=loL4I57hbHysPnlGByzpeZhkjZh6/g3eFo9XBwh0NFahtgySQ5gznZIie7sKhSjYx5 Cl11FZsYwKz56jgSG4oB3iZ1lprDMwzvqjUSZ5B3RfBFn+3vZdvcWWhlPiCi29NYODFI Kwo+j4aL4wA0wuqFbXv6ou5B8ZoFC2kAwau374xJ6EoWuXXyH0DmnHXwliTi7VMefDTx 0xqiqJTJSuocOQMOaFy0BtWSdxj0Wtd4e71qaRgJDhC2gQaQ4L3KqhyYUCBDBUiRcDCt ItkYCCJZjEkJ1Z+LWQ0PC9uv+W0nM/tmArEtF0wtKcwuD5LI5P0jpLzqzLIKMD9CrDWP aWEw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=73nE1OGN3cX8ujLhtyZhE/AevLnmpiTTMXVsEBTy/BM=; b=VLg7LMoq3hpn/Q0ZKM6fpnBGYjFEY+cGXbXivVDB450YBnqLVfNt0wQjjtuUNnsxpW XmxnpnLMVC25nbo35tRB9zLGuU/9qJ4UuloHaTgiqDFPvOWfMMeTl/dFo/FAPj1LmJu0 P+OxlcUg9JLh/isgawRFR+s+PoDMVbD0j30S+A9EboJH84PQ98s3vjMoYCxHABG2DBou zP0f3dkpROiFQbX6KOmFPT/1zxYoGzJE/RHvgRvFVB+R2yptOQtu9bh75ORanaaO2mt2 jUwZyuEM7ExhsQpdMn+uHyGWTnEZ+K/WWKHjz0ugfU0KneDEssSL1isrJbBgzFfdhxzb MH5g== X-Gm-Message-State: AO0yUKXICZTxxr2dwH8ZpspOfSWQXtUTzRrZ0cYmiZC69HQMD/psmGZU /c33BmGRctwgfqpsZ+l8plSA23exgTI= X-Google-Smtp-Source: AK7set/ZENXQwy5nYEN+BfYBNNU9N1cF3HF8788B9mJdZKd07i46nv0L8z9r8Dyjsql+K7bnc8N8AA== X-Received: by 2002:adf:e609:0:b0:2bf:d7bc:cd15 with SMTP id p9-20020adfe609000000b002bfd7bccd15mr2223524wrm.4.1675164981892; Tue, 31 Jan 2023 03:36:21 -0800 (PST) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id b14-20020a05600010ce00b0029e1aa67fd2sm14591650wrx.115.2023.01.31.03.36.21 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 31 Jan 2023 03:36:21 -0800 (PST) From: Simon Tournier To: Theodore Ehrenborg Subject: Re: bug#61121: Cannot import IJulia in Julia In-Reply-To: References: <87bkmgky0p.fsf@gmail.com> Date: Tue, 31 Jan 2023 12:34:16 +0100 Message-ID: <86o7qfuedj.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 61121 Cc: 61121@debbugs.gnu.org, Efraim Flashner X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, On Mon, 30 Jan 2023 at 21:55, Theodore Ehrenborg wrote: > Gentoo appears to have fixed this bug by linking julia/cert.pem to the > system's ca-certificates.crt. > https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3D26b59330b5222996de= fa4536237e62404bf21168 This trick is not possible, IIUC. > Is there a way I could rebuild my own slightly modified Julia with a link > like that? Maybe, by adding the package nss-certs as propagated-inputs in the definition of julia. > I understand that there's probably a good reason that Guix's Julia doesn't > by default have cert.pem, but I would be pleased with a hacky custom > solution if it made Jupyter notebooks work. The reason is security. ;-) It=E2=80=99s Julia that does poorly here. As pointed with the upstream package MbedTLS.jl, the fix should come from Julia itself; therefore, it could be worth to open an issue, if it is not already the case. ;-) >From my understanding, the culprit is this [1]: --8<---------------cut here---------------start------------->8--- function __init__() global artifact_dir =3D dirname(Sys.BINDIR) global cacert =3D normpath(Sys.BINDIR, Base.DATAROOTDIR, "julia", "cert= .pem") end --8<---------------cut here---------------end--------------->8--- And it is not clear for me if NetworkOptions.jl [2] provides the option of not, and I am missing why Julia itself does not depend on it. 1: https://github.com/JuliaLang/julia/blob/master/stdlib/MozillaCACerts_jll= /src/MozillaCACerts_jll.jl#L20 2: https://github.com/JuliaLang/NetworkOptions.jl Efraim, do you think it would be possible to patch Julia to point to some certificates via bundled_ca_roots or ca_roots_path? 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\\(\\) \\!=3D bundled_ca_roots\\(\\)") "@test_broken ca_roots_path() !=3D bundled_ca_roots()")) --8<---------------cut here---------------end--------------->8--- Cheers, simon From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 09 04:30:05 2023 Received: (at 61121) by debbugs.gnu.org; 9 Feb 2023 09:30:05 +0000 Received: from localhost ([127.0.0.1]:57527 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pQ3Fl-0001Of-8e for submit@debbugs.gnu.org; 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Thu, 09 Feb 2023 01:29:54 -0800 (PST) Date: Thu, 9 Feb 2023 11:29:53 +0200 From: Efraim Flashner To: Simon Tournier Subject: Re: bug#61121: Cannot import IJulia in Julia Message-ID: Mail-Followup-To: Efraim Flashner , Simon Tournier , Theodore Ehrenborg , 61121@debbugs.gnu.org References: <87bkmgky0p.fsf@gmail.com> <86o7qfuedj.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="W5mt5F0TvO9kpALK" Content-Disposition: inline In-Reply-To: <86o7qfuedj.fsf@gmail.com> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-Spam-Score: 0.3 (/) X-Debbugs-Envelope-To: 61121 Cc: 61121@debbugs.gnu.org, Theodore Ehrenborg X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) --W5mt5F0TvO9kpALK Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Tue, Jan 31, 2023 at 12:34:16PM +0100, Simon Tournier wrote: > Hi, >=20 > On Mon, 30 Jan 2023 at 21:55, Theodore Ehrenborg wrote: >=20 > > Gentoo appears to have fixed this bug by linking julia/cert.pem to the > > system's ca-certificates.crt. > > https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3D26b59330b5222996= defa4536237e62404bf21168 >=20 > This trick is not possible, IIUC. >=20 > > Is there a way I could rebuild my own slightly modified Julia with a li= nk > > like that? >=20 > Maybe, by adding the package nss-certs as propagated-inputs in the > definition of julia. By itself I don't think this would do anything. > > I understand that there's probably a good reason that Guix's Julia does= n't > > by default have cert.pem, but I would be pleased with a hacky custom > > solution if it made Jupyter notebooks work. >=20 > The reason is security. ;-) It=E2=80=99s Julia that does poorly here. >=20 > As pointed with the upstream package MbedTLS.jl, the fix should come > from Julia itself; therefore, it could be worth to open an issue, if it > is not already the case. ;-) >=20 > From my understanding, the culprit is this [1]: >=20 > --8<---------------cut here---------------start------------->8--- > function __init__() > global artifact_dir =3D dirname(Sys.BINDIR) > global cacert =3D normpath(Sys.BINDIR, Base.DATAROOTDIR, "julia", "ce= rt.pem") > end > --8<---------------cut here---------------end--------------->8--- >=20 > And it is not clear for me if NetworkOptions.jl [2] provides the option > of not, and I am missing why Julia itself does not depend on it. >=20 > 1: https://github.com/JuliaLang/julia/blob/master/stdlib/MozillaCACerts_j= ll/src/MozillaCACerts_jll.jl#L20 > 2: https://github.com/JuliaLang/NetworkOptions.jl >=20 >=20 > Efraim, do you think it would be possible to patch Julia to point to > some certificates via bundled_ca_roots or ca_roots_path? In the initial patch for julia-1.8.1 I think there was a substitution to hardcode /etc/ssl/something instead for 'global cacert' but I took that out since we don't like hardcoding that. GIT_SSL_CAINFO=3D/home/efraim/.guix-home/profile/etc/ssl/certs/ca-certifica= tes.crt SSL_CERT_DIR=3D/run/current-system/profile/etc/ssl/certs CURL_CA_BUNDLE=3D/home/efraim/.guix-home/profile/etc/ssl/certs/ca-certifica= tes.crt SSL_CERT_FILE=3D/run/current-system/profile/etc/ssl/certs/ca-certificates.c= rt I think it would be fine to tell Julia to look at SSL_CERT_FILE as the cacert so it can be overridden as desired, and then we can add a (native-?)search-path to Julia for SSL_CERT_FILE. Does anyone know offhand how to get the environment variable? If not I'll grep the sources and then look online. > Well, somehow turn back these tests: >=20 > --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 i= n network option > (substitute* "usr/share/julia/stdlib/v1.8/NetworkOptions/tes= t/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\\(\\) \\!=3D bundled_ca_roots\\(\\)= ") > "@test_broken ca_roots_path() !=3D bundled_ca_roots()")) > --8<---------------cut here---------------end--------------->8--- That one might be a little harder, I'd rather not add nss-certs to the build just for the test suite, but I'll see how it goes. Or at least update the comment afterward. >=20 > Cheers, > simon --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --W5mt5F0TvO9kpALK Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmPkvRAACgkQQarn3Mo9 g1H42g/+NBbSto/YVvqnqo1gX6zgFglkzfca4ROj4qznOnZ9ho16YHD+Y2r9tQO2 shkJUzx3XfR4S3Tn8gSwHVzLttk25hcDxDwYcjsiq15qPzfdtmlOubhDQ9PcHKxZ V51m6hyzwONDxH7mvgbBs1s+R/Sj3UQ6weS5zZ7KodB7wo2XMrfGPGckc+0lz8HO o+72HsQjuqKrFrdiiLkQ9rqAz8OE/4nVYRRSUSmICLOT/1EDHfMY9T1Ka3QZte1S YSAyLfey1/s5LFPo0jOcJxNVRAtfC8aqt1m4iOXo7Dpp+jbO8lZLVkloZflHxNjx oLuwfmri2z/WSCz61Crlk+q9mgwSE2/gDKpzonyi7+F5fzH2wNH5uKy6M124/kUE TXA5MBUcj+zAReMC0sctkzwHgIrAx8aSF6Cw1RgpY7GHCaOn9YqtoGYefntN5eDX +3nCuCssy5RMyXnNaVM+XZUvP1jTSbc6X+418pxKBZBA80H/mt2quLlALRIFFZ9G Mz2KHNf0QyW2Ome0Wj65Q7uYeTc3l4ncZVaK5hTFVn29kNWPnJGJXQTqEJ6htNTZ vrDLOdtYa/JDSQ7DppbbC4+piYBj9NgMolx0qEYPwOwLbxmYjtQaMtRfSYLd6SJ/ SA7o6HUhOOIuCQjGKhbWzc+NZS5Vg2L/FASwc7clheUr/lH99rY= =9cwu -----END PGP SIGNATURE----- --W5mt5F0TvO9kpALK-- From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 09 09:53:11 2023 Received: (at 61121-done) by debbugs.gnu.org; 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Thu, 09 Feb 2023 06:53:03 -0800 (PST) Date: Thu, 9 Feb 2023 16:53:01 +0200 From: Efraim Flashner To: Simon Tournier Subject: Re: bug#61121: Cannot import IJulia in Julia Message-ID: Mail-Followup-To: Efraim Flashner , Simon Tournier , Theodore Ehrenborg , 61121-done@debbugs.gnu.org References: <87bkmgky0p.fsf@gmail.com> <86o7qfuedj.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="eh/CUv0BbL+Ao3ps" Content-Disposition: inline In-Reply-To: <86o7qfuedj.fsf@gmail.com> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-Spam-Score: 0.2 (/) X-Debbugs-Envelope-To: 61121-done Cc: 61121-done@debbugs.gnu.org, Theodore Ehrenborg X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.8 (/) --eh/CUv0BbL+Ao3ps Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Tue, Jan 31, 2023 at 12:34:16PM +0100, Simon Tournier wrote: >=20 > --8<---------------cut here---------------start------------->8--- > function __init__() > global artifact_dir =3D dirname(Sys.BINDIR) > global cacert =3D normpath(Sys.BINDIR, Base.DATAROOTDIR, "julia", "ce= rt.pem") > end > --8<---------------cut here---------------end--------------->8--- I've changed this line to: global cacert =3D get(ENV, \"SSL_CERT_FILE\", "\"/etc/ssl/certs/ca-certific= ates.crt\") and then tested it with the example at the beginning of the bug report. > Well, somehow turn back these tests: >=20 > --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 i= n network option > (substitute* "usr/share/julia/stdlib/v1.8/NetworkOptions/tes= t/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\\(\\) \\!=3D bundled_ca_roots\\(\\)= ") > "@test_broken ca_roots_path() !=3D bundled_ca_roots()")) > --8<---------------cut here---------------end--------------->8--- I wasn't able to turn these tests back on though. --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --eh/CUv0BbL+Ao3ps Content-Type: application/pgp-signature; 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