* bug#61121: Cannot import IJulia in Julia @ 2023-01-28 13:45 Theodore Ehrenborg 2023-01-30 12:27 ` Simon Tournier 0 siblings, 1 reply; 6+ messages in thread From: Theodore Ehrenborg @ 2023-01-28 13:45 UTC (permalink / raw) To: 61121 [-- Attachment #1: Type: text/plain, Size: 1044 bytes --] 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 [-- Attachment #2: Type: text/html, Size: 1518 bytes --] ^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#61121: Cannot import IJulia in Julia 2023-01-28 13:45 bug#61121: Cannot import IJulia in Julia Theodore Ehrenborg @ 2023-01-30 12:27 ` Simon Tournier 2023-01-30 21:55 ` Theodore Ehrenborg 0 siblings, 1 reply; 6+ messages in thread From: Simon Tournier @ 2023-01-30 12:27 UTC (permalink / raw) To: Theodore Ehrenborg, 61121; +Cc: Efraim Flashner 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’s because Julia upstream does not take care about packagers; 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 ^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#61121: Cannot import IJulia in Julia 2023-01-30 12:27 ` Simon Tournier @ 2023-01-30 21:55 ` Theodore Ehrenborg 2023-01-31 11:34 ` Simon Tournier 0 siblings, 1 reply; 6+ messages in thread From: Theodore Ehrenborg @ 2023-01-30 21:55 UTC (permalink / raw) To: Simon Tournier; +Cc: 61121, Efraim Flashner [-- Attachment #1: Type: text/plain, Size: 1611 bytes --] 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=26b59330b5222996defa4536237e62404bf21168 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 mån 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/julia/cert.pem": > > No such file or directory > > [...] > > > I saw a very similar bug on Gentoo: > > [...] > > > (https://bugs.gentoo.org/888978) > > Well, that’s because Julia upstream does not take care about packagers; > 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 > [-- Attachment #2: Type: text/html, Size: 2523 bytes --] ^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#61121: Cannot import IJulia in Julia 2023-01-30 21:55 ` Theodore Ehrenborg @ 2023-01-31 11:34 ` Simon Tournier 2023-02-09 9:29 ` Efraim Flashner 2023-02-09 14:53 ` Efraim Flashner 0 siblings, 2 replies; 6+ messages in thread From: Simon Tournier @ 2023-01-31 11:34 UTC (permalink / raw) To: Theodore Ehrenborg; +Cc: 61121, Efraim Flashner Hi, On Mon, 30 Jan 2023 at 21:55, Theodore Ehrenborg <theodore.ehrenborg@gmail.com> 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=26b59330b5222996defa4536237e62404bf21168 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’s 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 = dirname(Sys.BINDIR) global cacert = 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\\(\\) \\!= bundled_ca_roots\\(\\)") "@test_broken ca_roots_path() != bundled_ca_roots()")) --8<---------------cut here---------------end--------------->8--- Cheers, simon ^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#61121: Cannot import IJulia in Julia 2023-01-31 11:34 ` Simon Tournier @ 2023-02-09 9:29 ` Efraim Flashner 2023-02-09 14:53 ` Efraim Flashner 1 sibling, 0 replies; 6+ messages in thread From: Efraim Flashner @ 2023-02-09 9:29 UTC (permalink / raw) To: Simon Tournier; +Cc: 61121, Theodore Ehrenborg [-- Attachment #1: Type: text/plain, Size: 4198 bytes --] On Tue, Jan 31, 2023 at 12:34:16PM +0100, Simon Tournier wrote: > Hi, > > On Mon, 30 Jan 2023 at 21:55, Theodore Ehrenborg <theodore.ehrenborg@gmail.com> 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=26b59330b5222996defa4536237e62404bf21168 > > 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. By itself I don't think this would do anything. > > 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’s 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 = dirname(Sys.BINDIR) > global cacert = 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? 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=/home/efraim/.guix-home/profile/etc/ssl/certs/ca-certificates.crt SSL_CERT_DIR=/run/current-system/profile/etc/ssl/certs CURL_CA_BUNDLE=/home/efraim/.guix-home/profile/etc/ssl/certs/ca-certificates.crt SSL_CERT_FILE=/run/current-system/profile/etc/ssl/certs/ca-certificates.crt 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: > > --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--- 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. > > Cheers, > simon -- Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 6+ messages in thread
* bug#61121: Cannot import IJulia in Julia 2023-01-31 11:34 ` Simon Tournier 2023-02-09 9:29 ` Efraim Flashner @ 2023-02-09 14:53 ` Efraim Flashner 1 sibling, 0 replies; 6+ messages in thread From: Efraim Flashner @ 2023-02-09 14:53 UTC (permalink / raw) To: Simon Tournier; +Cc: 61121-done, Theodore Ehrenborg [-- Attachment #1: Type: text/plain, Size: 1873 bytes --] 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@flashner.co.il> אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 6+ messages in thread
end of thread, other threads:[~2023-02-09 14:54 UTC | newest] Thread overview: 6+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2023-01-28 13:45 bug#61121: Cannot import IJulia in Julia Theodore Ehrenborg 2023-01-30 12:27 ` Simon Tournier 2023-01-30 21:55 ` Theodore Ehrenborg 2023-01-31 11:34 ` Simon Tournier 2023-02-09 9:29 ` Efraim Flashner 2023-02-09 14:53 ` Efraim Flashner
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