Received: (at 42920) by debbugs.gnu.org; 5 Apr 2022 15:00:33 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Apr 05 11:00:32 2022 Received: from localhost ([127.0.0.1]:55815 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nbkfY-0001Wb-HS for submit <at> debbugs.gnu.org; Tue, 05 Apr 2022 11:00:32 -0400 Received: from mta-15-3.privateemail.com ([198.54.122.111]:52292) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <dom@HIDDEN>) id 1nbkfW-0001WH-7U for 42920 <at> debbugs.gnu.org; Tue, 05 Apr 2022 11:00:31 -0400 Received: from mta-15.privateemail.com (localhost [127.0.0.1]) by mta-15.privateemail.com (Postfix) with ESMTP id 0584B18000AE; Tue, 5 Apr 2022 11:00:24 -0400 (EDT) DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=dominicm.dev; s=default; t=1649170824; bh=I+yazx12MzInnIYyxjOKOWUAhV7j6S2jegIcpV8VcWo=; h=References:From:To:Cc:Subject:Date:In-reply-to:From; b=jZrc3T5Sfz5UN5FS9ncHwsa68+3yY0r6iU36YqxCdT8qat13nZ8Fg6XSt7nkvExfz Ws1eCU5xAFeq+cYRGrkXqWw7yxzZxqlL2JV6nBHt7OciWseEv+kSEtC00HDg9uFPMp 9zJG28Wg3/dmajvVRs7L12wMpJzeKUH8WeVYq5VGY+Ztw5E3CmbtMCRRoWXEUJLNMO PW8tI8rE0muoVjxWGN1OKtpYGo8ttI94ywnuAw9KD7ZA2X8vGxTOjCLST/5bLTMCVC 5nXcYTbr4CZLAp+RrgaJGzlM/sCUjsfthE4/SR9qpWFXbpcwv9pWm8KDUnI/NeyU7g xZifmfuIH4/Qw== Received: from guix (unknown [10.20.151.182]) by mta-15.privateemail.com (Postfix) with ESMTPA id 3A70918000AD; Tue, 5 Apr 2022 11:00:22 -0400 (EDT) DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=dominicm.dev; s=default; t=1649170823; bh=I+yazx12MzInnIYyxjOKOWUAhV7j6S2jegIcpV8VcWo=; h=References:From:To:Cc:Subject:Date:In-reply-to:From; b=rdoxykSoZiSn1YEIcsFdy0ld5mUc6thmYO0PZi7r9eCW1LRP2fDzHtowB4qbphvej YRUarexWO9t6Py9aJm3rerOFh0wajGeYgZgUV7LqoS175jIevBmNx4Had0b0y9AD3Z AKaz9LMf51/zFGkuiTxBZGG12SygMijCKcLqMgtIv2eY57g3k673izUrA2BuiuiLaG YuJUs8kWmd5/V65O4GtascudOx966HMFLN6GszA3BNI7iGsaPbgM7YJQ0CWaQVQalC TaGentHlnYWJauETC6JcizNvUDzf3YEzhAPoJPsLBJhAbZ3LcHCQuLqz3WsUeyPF7m TmjiezHnpzg8w== References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <875yw3gj6w.fsf@HIDDEN> <86ee2bak4i.fsf@HIDDEN> <87fsmr3bl7.fsf@HIDDEN> User-agent: mu4e 1.6.10; emacs 27.2 From: Dominic Martinez <dom@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#42920: conda 4.8.3 on guix cannot activate environments Date: Tue, 05 Apr 2022 10:50:46 -0400 In-reply-to: <87fsmr3bl7.fsf@HIDDEN> Message-ID: <87tub7zibj.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Virus-Scanned: ClamAV using ClamSMTP X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 42920 Cc: 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable >> On Wed, 18 Aug 2021 at 12:07, Ricardo Wurmus=20 >> <rekado@HIDDEN> wrote: >>> We have since upgraded to 4.10.3, but the problems still=20 >>> persist. Conda still >>> asks users to run =E2=80=9Cconda init=E2=80=9D, which attempts to run = =E2=80=9Csudo=E2=80=9D=20 >>> to modify >>> root-owned files. It=E2=80=99s a big mess. I don't think conda init will ever work on Guix, and it seems out=20 of scope to try and prevent Conda from prompting users to do=20 that. I was able to get conda working with the following steps: 1. Expose the glibc interpreter so that conda python can function #+begin_src scheme (extra-special-file "/lib64/ld-linux-x86-64.so.2" (file-append glibc=20 "/lib/ld-linux-x86-64.so.2")) #+end_src 2. Source the conda environment variables. I do this both in my=20 profile (through home-shell-profile-service-type) and through my=20 rc file for interactive shells, as I think I remember having=20 problems not sourcing it in both. #+begin_src scheme (define-public (home-profile-service script) "Creates a service that sources a home profile.d script provided=20 by a package." (simple-service 'profile.d-service home-shell-profile-service-type `(,(plain-file (string-append script "-profile") (string-append "source=20 ~/.guix-home/profile/etc/profile.d/" script=20 ".sh"))))) (home-profile-service "conda") #+end_src #+begin_src shell source ~/.guix-home/profile/etc/profile.d/conda.sh #+end_src I agree that this setup is not ideal, but I think that guix home=20 has the promise of fixing a lot of these issues with home=20 services! Hopefully in the near future we'll be able to turn these=20 fixed into services for users. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQRtp6gAxeTcYmhxQ/1Bnl1fEVBrXQUCYkxZgAAKCRBBnl1fEVBr XW/0AP4+CQd9Qlwnr1MlsXvUpLIJ9r9ZZjm4bLCr9AaVIVKq2QD/f+EPnIxE4bK5 +MvM8wLsNW55LOv8WdzUCA4Y+E9JKgE= =iIhj -----END PGP SIGNATURE----- --=-=-=--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 5 Apr 2022 13:26:55 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Apr 05 09:26:55 2022 Received: from localhost ([127.0.0.1]:54096 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nbjCw-0004h7-QU for submit <at> debbugs.gnu.org; Tue, 05 Apr 2022 09:26:54 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21038) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1nbjCv-0004gz-BI for 42920 <at> debbugs.gnu.org; Tue, 05 Apr 2022 09:26:53 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649165210; cv=none; d=zohomail.com; s=zohoarc; b=J2QNtoAuStedsoedBEUoIHvQ00fLBd/toHF/Kdads/IQjpkcG0KI6cDLgPTHrhd13ITK94bs04rjna4z7QNrabm5m7PsjfpXuTZLYAvA9d2r2IMCctL/u/KkRtINBxnaCSblR4cgG+S0abcuxNJxm5rld1gIj3suCI1uNHFhD5I= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649165210; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=R5DSD3HErDfeGc0vK4ZwgR8KGjEU1UTydMvsOG9btm0=; b=H3LRo78EsPwl6MwDrj6Pom7eLODC/bAJe2+OAxptShbEVEC6gFJ/us+7AcB3vePY1fWExiUAzWVNteYjleRl1cK8Yq8+KX3fu/cGnq2cVpR2CK8Dl7DNp7K0f8DnvsMMyktiwcY6G34jE0L+61eqL/0nrJg+dPJrLuUFJCfzOj0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1649165210; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=R5DSD3HErDfeGc0vK4ZwgR8KGjEU1UTydMvsOG9btm0=; b=Oa9gB762iNLCUo1Qfg/LfKZqvzaymkJvnJGmjqHRG5SDni4S1h1ghukz0TQhwzGe XJyN/IoPusinwt4flSrIlaFEFxtnTjJw9P+lcTm6ZD3JfmVvsixST8aMlSSMxZU+E8X cg/e6Nbpqy00hfU0mIgU8Wdl1j6005lnxzWjeOpU= Received: from localhost (248-110-142-46.pool.kielnet.net [46.142.110.248]) by mx.zohomail.com with SMTPS id 164916520803513.657709036017536; Tue, 5 Apr 2022 06:26:48 -0700 (PDT) References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <875yw3gj6w.fsf@HIDDEN> <86ee2bak4i.fsf@HIDDEN> User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus <rekado@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#42920: conda 4.8.3 on guix cannot activate environments Date: Tue, 05 Apr 2022 15:26:15 +0200 In-reply-to: <86ee2bak4i.fsf@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87fsmr3bl7.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 42920 Cc: 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) zimoun <zimon.toutoune@HIDDEN> writes: > On Wed, 18 Aug 2021 at 12:07, Ricardo Wurmus <rekado@HIDDEN> wrote: >> We have since upgraded to 4.10.3, but the problems still persist. Conda = still >> asks users to run =E2=80=9Cconda init=E2=80=9D, which attempts to run = =E2=80=9Csudo=E2=80=9D to modify >> root-owned files. It=E2=80=99s a big mess. > > What is the point to have Conda installed by Guix? Convenience. --=20 Ricardo
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 5 Apr 2022 10:48:11 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Apr 05 06:48:11 2022 Received: from localhost ([127.0.0.1]:53822 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nbgjL-0006En-N9 for submit <at> debbugs.gnu.org; Tue, 05 Apr 2022 06:48:11 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:41555) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1nbgjJ-0006Ea-89 for 42920 <at> debbugs.gnu.org; Tue, 05 Apr 2022 06:48:10 -0400 Received: by mail-wr1-f53.google.com with SMTP id k23so6105071wrd.8 for <42920 <at> debbugs.gnu.org>; Tue, 05 Apr 2022 03:48:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version:content-transfer-encoding; bh=KPEJrTj+BPGWj+EpBZ+kHnuHogqJGiCTZ1xGOU5USeg=; b=SjGKMfqbgTJeGb9NL1bsJ+YUuLNA0tPQL0v7fqe79rytAn1OzLWu4JHsJ+WU4wsJQT sbXH7mwZ8pq/gqLNx9hczvJxme00cEy1F4JOf8L+4qgDGFo3IgRlr1162irsKxxmOthG XADc5Q3aCAmpe46eSxFvFNAT552LwphX1P30cx3uGW5D8nIH45eb59T7b8x6gEaRICqT 0CPgGzuMXoVHqU1BugqvAkBFN88+S8HJhnOWTt0OysS2qiy0P2oAD95CMhy5bpPygLh/ OMwZZSEqCxUMO6j50iVavtN22I9CO4C7Une9jdNwCOVQplpb75dnZKAKLxi7k651p6cz h2Qw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version:content-transfer-encoding; bh=KPEJrTj+BPGWj+EpBZ+kHnuHogqJGiCTZ1xGOU5USeg=; b=Q9QYkoZsDxW3vdVxYDS8rSU/ncifWfhf/Dy24u05errLTKBy4cjlhPYiAyUhMq7Uv8 +zXM+F8GeggSdcADgmfpJPPd8bp+2GHFCP3KIFiPfJRuLsNX8gvMaC9pXDjuI/Jd7uUU tMBlmNTAvr+0gtZqAYZWDQkc2Pb34SH/xdvHQUTfLAsP3FJTYaF9KA1AiZO6iAzM5CTO 48NYjYkxDGliFU3AWw+/z+vIplE6AhwcsG7iSRFviZ5fA362vF8ddPeSCIb7F1fgNoCw 6CMOWjO6kDK2+fXtmlYbIWPYM6aaxlumHhgZG9LiJkNwutMMcNcnipX1HCZ4SXGAgZ4g ubbg== X-Gm-Message-State: AOAM531U3w85/xk33Et2oZYDkKf13bCd0jTQp5bxPGPG3ApUBJs8vBu+ PLAd4fZ9wyiVTk9QZcMLfM8U223dM4o= X-Google-Smtp-Source: ABdhPJzADzY5MN64pjHkHej8aotcz0QQyQ/99DV7JGOfEX3BdHUxDhAgNOr1sDIKMXqfm/iR6Am/rw== X-Received: by 2002:a5d:6da7:0:b0:205:7ccc:a001 with SMTP id u7-20020a5d6da7000000b002057ccca001mr2216124wrs.389.1649155682832; Tue, 05 Apr 2022 03:48:02 -0700 (PDT) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id 10-20020a5d47aa000000b00204012e4373sm13282435wrb.101.2022.04.05.03.48.01 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 05 Apr 2022 03:48:02 -0700 (PDT) From: zimoun <zimon.toutoune@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#42920: conda 4.8.3 on guix cannot activate environments References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <875yw3gj6w.fsf@HIDDEN> Date: Tue, 05 Apr 2022 12:40:29 +0200 In-Reply-To: <875yw3gj6w.fsf@HIDDEN> (Ricardo Wurmus's message of "Wed, 18 Aug 2021 12:07:19 +0200") Message-ID: <86ee2bak4i.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) 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: 42920 Cc: 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hi Ricardo, On Wed, 18 Aug 2021 at 12:07, Ricardo Wurmus <rekado@HIDDEN> wrote: > We have since upgraded to 4.10.3, but the problems still persist. Conda s= till > asks users to run =E2=80=9Cconda init=E2=80=9D, which attempts to run =E2= =80=9Csudo=E2=80=9D to modify > root-owned files. It=E2=80=99s a big mess. What is the point to have Conda installed by Guix? Cheers, simon
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 18 Aug 2021 10:07:39 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Aug 18 06:07:39 2021 Received: from localhost ([127.0.0.1]:54919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1mGITv-0007fv-Kj for submit <at> debbugs.gnu.org; Wed, 18 Aug 2021 06:07:39 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21198) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1mGITq-0007fd-34 for 42920 <at> debbugs.gnu.org; Wed, 18 Aug 2021 06:07:34 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1629281245; cv=none; d=zohomail.com; s=zohoarc; b=IBVaX4eZJdOpycjQ87UX1XDSQ9MDuDWHZkKIf3Ea4NoxDopQdA7ABhGKPnexeZOCebmNeq1UShlObZ5XqG3gYsIeRPp8Waa1S2htJ3x88VIV8jFja8pfr7TkTkPs4jF2Yh4Cf8+hLqM0DTPAQI+1i+FS+NXPI9472wxZ+TiFNxQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1629281245; h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To; bh=2uO7NvnuooZDYPh8hbDW98ygL9s3/sw/SPQ5Zri5IuY=; b=fGrnfFmoAfKhV2gFIhMiIiuV8sWPveqSNh6Eb5jPfIJ1pdF+3n94lm22vOyKkRWSjooprgoRuQELozVu7OlSAwAFW5SK8o+guOxOqH4u5pWLBTjbbengayRg+DfeFsf+vKgLL1Ax69DhAi4/WPmlmavnsFuZNOb8oqcwly1zueo= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1629281245; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=From:To:Subject:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=2uO7NvnuooZDYPh8hbDW98ygL9s3/sw/SPQ5Zri5IuY=; b=CeAvAxDsJFNjZ0AHcO09Xt7iXVxhgxwbSHXHJe+cWnocvSOftwx1hnnnuTWzY1+h /ImpxxYSuTPU4uLvJ46jkSNwjdazmQYbu7zUfegk+OAQIggh5q2DKksncKWz6B4VgNE HXfL3nZ5oFI2qF9vPmsWc+0FDtIRE8rV24aAfiH8= Received: from localhost (p54ad4ffc.dip0.t-ipconnect.de [84.173.79.252]) by mx.zohomail.com with SMTPS id 1629281242336900.9782159638067; Wed, 18 Aug 2021 03:07:22 -0700 (PDT) User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus <rekado@HIDDEN> To: 42920 <at> debbugs.gnu.org Subject: conda 4.8.3 on guix cannot activate environments X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 18 Aug 2021 12:07:19 +0200 Message-ID: <875yw3gj6w.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 42920 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) We have since upgraded to 4.10.3, but the problems still persist.=20 Conda still asks users to run =E2=80=9Cconda init=E2=80=9D, which attempts = to run=20 =E2=80=9Csudo=E2=80=9D to modify root-owned files. It=E2=80=99s a big mess. Any ideas? --=20 Ricardo
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 1 Mar 2021 18:50:38 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Mar 01 13:50:38 2021 Received: from localhost ([127.0.0.1]:50772 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1lGncs-0001S3-6M for submit <at> debbugs.gnu.org; Mon, 01 Mar 2021 13:50:38 -0500 Received: from mail-pj1-f44.google.com ([209.85.216.44]:38660) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1lGncl-0001Rd-7H for 42920 <at> debbugs.gnu.org; Mon, 01 Mar 2021 13:50:32 -0500 Received: by mail-pj1-f44.google.com with SMTP id l18so154260pji.3 for <42920 <at> debbugs.gnu.org>; Mon, 01 Mar 2021 10:50:31 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=PPeHai1a3TxBBuOo0aVpeA7X6+PbTjT5YaCFLwVMGgU=; b=ovtwLxoMP+73dOY3bJqe3VVqlcBKb8GaekufP/2EAawksx+9hEw+dQWul2qAhL1VGZ ymGqxRqL1ecoPVFl1SJu/tJFAk+gYRkPwE8v9WQj8hVHZV+Ua+zgUAuyP+k2MfGv+w4P LloqN5FmSkq2bzA07ITgUyBcJl/mbdIwkMB5SkrA3J90Dd98RxMfajVQROtk2oaKn22c Xb+EibmvrFLsGaBI+SgMMOzPI6vI3DOtWQDj4z/78XZGHHN4JFmK0zRl4ecBedd5NR9c lANQEFJW74rXzakuXdWI6AJVTPC6S2eCBddZMvLpl7BDpbCfwh+JaQ/JNAuA788jSf8T dq+w== X-Gm-Message-State: AOAM532gUvRUqZA0ZTeQRbTPz71POfFFGTolG2xpyM2wCn6AnWnjyyn7 yYBjVf0jXmYyVPAjRNb3Oy3pvaD7/gbWY3L8/2Elp7nyx8GRuQ== X-Google-Smtp-Source: ABdhPJxg7fuMp3lxK30Q+yzvsmQpl0ZC4p8UfqiKt7RXR/Vghk1QU2ahZU3JEQ6XJ96ZzwWzdaV1X+zAeVJXmZpXNbI= X-Received: by 2002:a17:902:9b91:b029:e3:2c9e:f511 with SMTP id y17-20020a1709029b91b02900e32c9ef511mr16964985plp.74.1614624625134; Mon, 01 Mar 2021 10:50:25 -0800 (PST) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> <87imd6x5to.fsf@HIDDEN> <CA+Jv8O1uj5XrWk6PnO4UCwjBPxmfV+4QM_+uosP71POG6vkyTg@HIDDEN> In-Reply-To: <CA+Jv8O1uj5XrWk6PnO4UCwjBPxmfV+4QM_+uosP71POG6vkyTg@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Mon, 1 Mar 2021 19:50:13 +0100 Message-ID: <CA+Jv8O2Pt8snedGMPX3cvxOowp3=04trxLO5sTpt-bb0nGY0iA@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="0000000000003a0e4905bc7e17c8" X-Spam-Score: 0.5 (/) X-Debbugs-Envelope-To: 42920 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.5 (/) --0000000000003a0e4905bc7e17c8 Content-Type: text/plain; charset="UTF-8" Hi Ricardo et al., I've not yet looked into updating the conda package, but want to add a small thing to the bug report, so it can easily be found. Lines in the sourced conda.sh script like the one below won't work anymore once the conda executable is wrapped in the guix shell script, because PS1 is eaten by the wrapper: "$CONDA_EXE" $_CE_M $_CE_CONDA It is necessary to explicitly call bash in interactive mode to have PS1 available: bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA However, that will add every executed line to the .bash_history file, including very long "export PYTHONPATH" lines. This can be avoided by explicitly setting the history file to nothing: HISTFILE= bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA Cheers, Hugo On Tue, 25 Aug 2020 at 17:03, Hugo Buddelmeijer <hugo@HIDDEN> wrote: > Hi Ricardo, > > On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <rekado@HIDDEN> wrote: > >> >> > The problem with the prompt arises from step 4), because 'conda' has >> bash >> > as interpreter, and "non-interactive bashes go out of their way to unset >> > PS1": >> > >> https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1 >> > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html >> >> Good sleuthing! >> >> > So .conda.real never gets the PS1 variable and it disappears. > > > I did some more experiments, and forcing the wrapper script to start in > interactive mode solves the problem. > > `conda init` adds some things to `.bashrc`, in particular it `eval`s the > output from `conda shell.bash hook`, which creates the `conda` bash > function (and associated functions). > > The output from `conda shell.bash hook` seems to be based on > `/etc/profile.d/conda.sh`: > > https://github.com/conda/conda/blob/master/conda/shell/etc/profile.d/conda.sh > As in, it prefixes some environment variables and appends the activation > of the base environment. > > Now if we replace all 5 occurances of > "$CONDA_EXE" $_CE_M $_CE_CONDA > in that file with > bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA > then everything works as expected. > > The -i is to enable interactive mode, preventing PS1 from being eaten. > --norc is necessary to not source .bashrc. > There are two occurences of "$CONDA_EXE" that should not be replaced, > hence adding the CE variables. > > Would editing files like that be possible in a guix package script? > > It seems that it is only a simple sed replace on a single file. It is a > bit hackish, because it adds knowledge to the package that a) there is a > wrapper script and b) it is in bash. > > I have only experimented with it by copying the output off `conda > shell.bash hook` to a file in my home directory and editing that. Maybe I > can try to update the package too. > > Other options: > - Use some other sh than bash, one that does not eat PS1, (e.g. dash) as > wrapper script. I just verified that *all* wrappers on my machine are bash. > However, some are using bash-minimal, so that means that there is a choice, > so maybe switching shells is possible? > - Somehow let conda work with another variable than PS1. Seems more > complicated. > > Then what is left is updating `conda init` such that > - it doesn't complain when it cannot edit files > - it only uses paths in ~/.guix-profile > but this is not essential to get conda to work. > > Cheers, > Hugo > > --0000000000003a0e4905bc7e17c8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hi Ricardo et al.,</div><div><br></div><div>I've = not yet looked into updating the conda package, but want to add a small thi= ng to the bug report, so it can easily be found.<br></div><div><br></div><d= iv>Lines in the sourced conda.sh script like the one below won't work a= nymore once the conda executable is wrapped in the guix shell script, becau= se PS1 is eaten by the wrapper:</div><div><br></div><div><div>=C2=A0=C2=A0= =C2=A0 "$CONDA_EXE" $_CE_M $_CE_CONDA</div></div><div><br></div><= div>It is necessary to explicitly call bash in interactive mode to have PS1= available:</div><div><br></div><div><div>=C2=A0=C2=A0=C2=A0 bash --<span c= lass=3D"gmail-il">norc</span> -i "$CONDA_EXE" $_CE_M $_CE_CONDA</= div></div><div><br></div><div>However, that will add every executed line to= the .bash_history file, including very long "export PYTHONPATH" = lines. This can be avoided by explicitly setting the history file to nothin= g:<br></div><div><br></div><div><div><div>=C2=A0=C2=A0=C2=A0 HISTFILE=3D ba= sh --<span class=3D"gmail-il">norc</span> -i "$CONDA_EXE" $_CE_M = $_CE_CONDA</div></div></div><div><br></div><div>Cheers,</div><div>Hugo<br><= /div><div><br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" c= lass=3D"gmail_attr">On Tue, 25 Aug 2020 at 17:03, Hugo Buddelmeijer <<a = href=3D"mailto:hugo@HIDDEN">hugo@HIDDEN</a>> wrote:<br= ></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;= border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><= div>Hi Ricardo,<br></div><br><div><div dir=3D"ltr" class=3D"gmail_attr">On = Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <<a href=3D"mailto:rekado@elep= hly.net" target=3D"_blank">rekado@HIDDEN</a>> wrote:<br></div><bloc= kquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:= 1px solid rgb(204,204,204);padding-left:1ex"><br> > The problem with the prompt arises from step 4), because 'conda= 9; has bash<br> > as interpreter, and "non-interactive bashes go out of their way t= o unset<br> > PS1":<br> > <a href=3D"https://superuser.com/questions/663069/why-does-subshell-no= t-inherit-exported-variable-ps1" rel=3D"noreferrer" target=3D"_blank">https= ://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-va= riable-ps1</a><br> > <a href=3D"https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html" rel=3D= "noreferrer" target=3D"_blank">https://tldp.org/HOWTO/Bash-Prompt-HOWTO/set= ps.html</a><br> <br> Good sleuthing!<br> <br> > So .conda.real never gets the PS1 variable and it disappears.</blockqu= ote><div><br></div><div>I did some more experiments, and forcing the wrappe= r script to start in interactive mode solves the problem.</div><div><br></d= iv>`conda init` adds some things to `.bashrc`, in particular it `eval`s the= output from `conda shell.bash hook`, which creates the `conda` bash functi= on (and associated functions).</div><div><br></div><div>The output from `co= nda shell.bash hook` seems to be based on `/etc/profile.d/conda.sh`:<br></d= iv><div><a href=3D"https://github.com/conda/conda/blob/master/conda/shell/e= tc/profile.d/conda.sh" target=3D"_blank">https://github.com/conda/conda/blo= b/master/conda/shell/etc/profile.d/conda.sh</a></div><div>As in, it prefixe= s some environment variables and appends the activation of the base environ= ment.</div><div><br></div><div>Now if we replace all 5 occurances of</div><= div>"$CONDA_EXE" $_CE_M $_CE_CONDA</div><div>in that file with</d= iv><div>bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA</div><div>t= hen everything works as expected.</div><div><br></div><div>The -i is to ena= ble interactive mode, preventing PS1 from being eaten. --norc is necessary = to not source .bashrc.<br></div><div>There are two occurences of "$CON= DA_EXE" that should not be replaced, hence adding the CE variables.</d= iv><div><br></div><div>Would editing files like that be possible in a guix = package script?</div><div><br></div><div><div>It seems that it is only a si= mple sed replace on a single file. It is a bit hackish, because it adds kno= wledge to the package that a) there is a wrapper script and b) it is in bas= h.</div></div><div><br></div><div>I have only experimented with it by copyi= ng the output off `conda shell.bash hook` to a file in my home directory an= d editing that. Maybe I can try to update the package too.<br></div><div><b= r></div><div>Other options:</div><div>- Use some other sh than bash, one th= at does not eat PS1, (e.g. dash) as wrapper script. I just verified that *a= ll* wrappers on my machine are bash. However, some are using bash-minimal, = so that means that there is a choice, so maybe switching shells is possible= ?</div><div>- Somehow let conda work with another variable than PS1. Seems = more complicated.</div><div><br></div><div>Then what is left is updating `c= onda init` such that</div><div>- it doesn't complain when it cannot edi= t files</div><div>- it only uses paths in ~/.guix-profile</div><div>but thi= s is not essential to get conda to work.<br></div><div><br></div><div>Cheer= s,</div><div>Hugo</div><div><br></div></div> </blockquote></div> --0000000000003a0e4905bc7e17c8--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at submit) by debbugs.gnu.org; 1 Mar 2021 18:50:38 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Mar 01 13:50:38 2021 Received: from localhost ([127.0.0.1]:50770 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1lGncn-0001Rx-Ud for submit <at> debbugs.gnu.org; Mon, 01 Mar 2021 13:50:38 -0500 Received: from lists.gnu.org ([209.51.188.17]:41380) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1lGncl-0001Rj-Aq for submit <at> debbugs.gnu.org; Mon, 01 Mar 2021 13:50:32 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:35418) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1lGnck-0002VH-6k for bug-guix@HIDDEN; Mon, 01 Mar 2021 13:50:30 -0500 Received: from mail-pl1-f182.google.com ([209.85.214.182]:36036) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1lGnch-0008OU-N6 for bug-guix@HIDDEN; Mon, 01 Mar 2021 13:50:29 -0500 Received: by mail-pl1-f182.google.com with SMTP id e9so10477830plh.3 for <bug-guix@HIDDEN>; Mon, 01 Mar 2021 10:50:26 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=PPeHai1a3TxBBuOo0aVpeA7X6+PbTjT5YaCFLwVMGgU=; b=iJyIQ1RDNgzV6dJDRLsCVJ8ywrBr+8VCzKSdUARVpF5WJECCte8FRo+nxEl/nr9wSW 0sSLKyN6eBZTmQBSr6R74s67fhoD5o7a091qLpw4FPq9hvRDLiTLG0EPO0DRBrd5T6Vv YmRIYUi+xrBMY6rLFYrAohU5ektl+6UtDvCAjTGF39Tx7unA+9nJNNEmPVoq8ET8nSNx L+ArHJ+IDH9XSpzSPHJYg+EbX1OZSTgVUgZvpcyQ7Si6RPv1C0TtmCT1b5Mz/rzsElCj 4zjTfFkGDd6M30y0RCaLHo3dRWwNLEvkeiM1J4+JJzPpAHphvW2CllW/p6dY8vA8eE9T Mwlw== X-Gm-Message-State: AOAM53247UbcjXZ087JpwtmeC2/itbw0xYarvTn+IZGnGD09Dvv2BTx+ BobXpsMNzAD99e6KVTrCww11s5Yv1y/FT28n5hk= X-Google-Smtp-Source: ABdhPJxg7fuMp3lxK30Q+yzvsmQpl0ZC4p8UfqiKt7RXR/Vghk1QU2ahZU3JEQ6XJ96ZzwWzdaV1X+zAeVJXmZpXNbI= X-Received: by 2002:a17:902:9b91:b029:e3:2c9e:f511 with SMTP id y17-20020a1709029b91b02900e32c9ef511mr16964985plp.74.1614624625134; Mon, 01 Mar 2021 10:50:25 -0800 (PST) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> <87imd6x5to.fsf@HIDDEN> <CA+Jv8O1uj5XrWk6PnO4UCwjBPxmfV+4QM_+uosP71POG6vkyTg@HIDDEN> In-Reply-To: <CA+Jv8O1uj5XrWk6PnO4UCwjBPxmfV+4QM_+uosP71POG6vkyTg@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Mon, 1 Mar 2021 19:50:13 +0100 Message-ID: <CA+Jv8O2Pt8snedGMPX3cvxOowp3=04trxLO5sTpt-bb0nGY0iA@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="0000000000003a0e4905bc7e17c8" Received-SPF: pass client-ip=209.85.214.182; envelope-from=blackshift@HIDDEN; helo=mail-pl1-f182.google.com X-Spam_score_int: -13 X-Spam_score: -1.4 X-Spam_bar: - X-Spam_report: (-1.4 / 5.0 requ) BAYES_00=-1.9, FREEMAIL_FORGED_FROMDOMAIN=0.25, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=0.249, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.8 (/) X-Debbugs-Envelope-To: submit Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: 0.5 (/) --0000000000003a0e4905bc7e17c8 Content-Type: text/plain; charset="UTF-8" Hi Ricardo et al., I've not yet looked into updating the conda package, but want to add a small thing to the bug report, so it can easily be found. Lines in the sourced conda.sh script like the one below won't work anymore once the conda executable is wrapped in the guix shell script, because PS1 is eaten by the wrapper: "$CONDA_EXE" $_CE_M $_CE_CONDA It is necessary to explicitly call bash in interactive mode to have PS1 available: bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA However, that will add every executed line to the .bash_history file, including very long "export PYTHONPATH" lines. This can be avoided by explicitly setting the history file to nothing: HISTFILE= bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA Cheers, Hugo On Tue, 25 Aug 2020 at 17:03, Hugo Buddelmeijer <hugo@HIDDEN> wrote: > Hi Ricardo, > > On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <rekado@HIDDEN> wrote: > >> >> > The problem with the prompt arises from step 4), because 'conda' has >> bash >> > as interpreter, and "non-interactive bashes go out of their way to unset >> > PS1": >> > >> https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1 >> > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html >> >> Good sleuthing! >> >> > So .conda.real never gets the PS1 variable and it disappears. > > > I did some more experiments, and forcing the wrapper script to start in > interactive mode solves the problem. > > `conda init` adds some things to `.bashrc`, in particular it `eval`s the > output from `conda shell.bash hook`, which creates the `conda` bash > function (and associated functions). > > The output from `conda shell.bash hook` seems to be based on > `/etc/profile.d/conda.sh`: > > https://github.com/conda/conda/blob/master/conda/shell/etc/profile.d/conda.sh > As in, it prefixes some environment variables and appends the activation > of the base environment. > > Now if we replace all 5 occurances of > "$CONDA_EXE" $_CE_M $_CE_CONDA > in that file with > bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA > then everything works as expected. > > The -i is to enable interactive mode, preventing PS1 from being eaten. > --norc is necessary to not source .bashrc. > There are two occurences of "$CONDA_EXE" that should not be replaced, > hence adding the CE variables. > > Would editing files like that be possible in a guix package script? > > It seems that it is only a simple sed replace on a single file. It is a > bit hackish, because it adds knowledge to the package that a) there is a > wrapper script and b) it is in bash. > > I have only experimented with it by copying the output off `conda > shell.bash hook` to a file in my home directory and editing that. Maybe I > can try to update the package too. > > Other options: > - Use some other sh than bash, one that does not eat PS1, (e.g. dash) as > wrapper script. I just verified that *all* wrappers on my machine are bash. > However, some are using bash-minimal, so that means that there is a choice, > so maybe switching shells is possible? > - Somehow let conda work with another variable than PS1. Seems more > complicated. > > Then what is left is updating `conda init` such that > - it doesn't complain when it cannot edit files > - it only uses paths in ~/.guix-profile > but this is not essential to get conda to work. > > Cheers, > Hugo > > --0000000000003a0e4905bc7e17c8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hi Ricardo et al.,</div><div><br></div><div>I've = not yet looked into updating the conda package, but want to add a small thi= ng to the bug report, so it can easily be found.<br></div><div><br></div><d= iv>Lines in the sourced conda.sh script like the one below won't work a= nymore once the conda executable is wrapped in the guix shell script, becau= se PS1 is eaten by the wrapper:</div><div><br></div><div><div>=C2=A0=C2=A0= =C2=A0 "$CONDA_EXE" $_CE_M $_CE_CONDA</div></div><div><br></div><= div>It is necessary to explicitly call bash in interactive mode to have PS1= available:</div><div><br></div><div><div>=C2=A0=C2=A0=C2=A0 bash --<span c= lass=3D"gmail-il">norc</span> -i "$CONDA_EXE" $_CE_M $_CE_CONDA</= div></div><div><br></div><div>However, that will add every executed line to= the .bash_history file, including very long "export PYTHONPATH" = lines. This can be avoided by explicitly setting the history file to nothin= g:<br></div><div><br></div><div><div><div>=C2=A0=C2=A0=C2=A0 HISTFILE=3D ba= sh --<span class=3D"gmail-il">norc</span> -i "$CONDA_EXE" $_CE_M = $_CE_CONDA</div></div></div><div><br></div><div>Cheers,</div><div>Hugo<br><= /div><div><br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" c= lass=3D"gmail_attr">On Tue, 25 Aug 2020 at 17:03, Hugo Buddelmeijer <<a = href=3D"mailto:hugo@HIDDEN">hugo@HIDDEN</a>> wrote:<br= ></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;= border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><= div>Hi Ricardo,<br></div><br><div><div dir=3D"ltr" class=3D"gmail_attr">On = Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <<a href=3D"mailto:rekado@elep= hly.net" target=3D"_blank">rekado@HIDDEN</a>> wrote:<br></div><bloc= kquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:= 1px solid rgb(204,204,204);padding-left:1ex"><br> > The problem with the prompt arises from step 4), because 'conda= 9; has bash<br> > as interpreter, and "non-interactive bashes go out of their way t= o unset<br> > PS1":<br> > <a href=3D"https://superuser.com/questions/663069/why-does-subshell-no= t-inherit-exported-variable-ps1" rel=3D"noreferrer" target=3D"_blank">https= ://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-va= riable-ps1</a><br> > <a href=3D"https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html" rel=3D= "noreferrer" target=3D"_blank">https://tldp.org/HOWTO/Bash-Prompt-HOWTO/set= ps.html</a><br> <br> Good sleuthing!<br> <br> > So .conda.real never gets the PS1 variable and it disappears.</blockqu= ote><div><br></div><div>I did some more experiments, and forcing the wrappe= r script to start in interactive mode solves the problem.</div><div><br></d= iv>`conda init` adds some things to `.bashrc`, in particular it `eval`s the= output from `conda shell.bash hook`, which creates the `conda` bash functi= on (and associated functions).</div><div><br></div><div>The output from `co= nda shell.bash hook` seems to be based on `/etc/profile.d/conda.sh`:<br></d= iv><div><a href=3D"https://github.com/conda/conda/blob/master/conda/shell/e= tc/profile.d/conda.sh" target=3D"_blank">https://github.com/conda/conda/blo= b/master/conda/shell/etc/profile.d/conda.sh</a></div><div>As in, it prefixe= s some environment variables and appends the activation of the base environ= ment.</div><div><br></div><div>Now if we replace all 5 occurances of</div><= div>"$CONDA_EXE" $_CE_M $_CE_CONDA</div><div>in that file with</d= iv><div>bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA</div><div>t= hen everything works as expected.</div><div><br></div><div>The -i is to ena= ble interactive mode, preventing PS1 from being eaten. --norc is necessary = to not source .bashrc.<br></div><div>There are two occurences of "$CON= DA_EXE" that should not be replaced, hence adding the CE variables.</d= iv><div><br></div><div>Would editing files like that be possible in a guix = package script?</div><div><br></div><div><div>It seems that it is only a si= mple sed replace on a single file. It is a bit hackish, because it adds kno= wledge to the package that a) there is a wrapper script and b) it is in bas= h.</div></div><div><br></div><div>I have only experimented with it by copyi= ng the output off `conda shell.bash hook` to a file in my home directory an= d editing that. Maybe I can try to update the package too.<br></div><div><b= r></div><div>Other options:</div><div>- Use some other sh than bash, one th= at does not eat PS1, (e.g. dash) as wrapper script. I just verified that *a= ll* wrappers on my machine are bash. However, some are using bash-minimal, = so that means that there is a choice, so maybe switching shells is possible= ?</div><div>- Somehow let conda work with another variable than PS1. Seems = more complicated.</div><div><br></div><div>Then what is left is updating `c= onda init` such that</div><div>- it doesn't complain when it cannot edi= t files</div><div>- it only uses paths in ~/.guix-profile</div><div>but thi= s is not essential to get conda to work.<br></div><div><br></div><div>Cheer= s,</div><div>Hugo</div><div><br></div></div> </blockquote></div> --0000000000003a0e4905bc7e17c8--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 25 Aug 2020 15:03:46 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Aug 25 11:03:46 2020 Received: from localhost ([127.0.0.1]:35671 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1kAaUD-0004yc-Up for submit <at> debbugs.gnu.org; Tue, 25 Aug 2020 11:03:46 -0400 Received: from mail-pg1-f175.google.com ([209.85.215.175]:34937) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1kAaUB-0004yO-AI for 42920 <at> debbugs.gnu.org; Tue, 25 Aug 2020 11:03:44 -0400 Received: by mail-pg1-f175.google.com with SMTP id o5so7014386pgb.2 for <42920 <at> debbugs.gnu.org>; Tue, 25 Aug 2020 08:03:43 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=vuwKIn4ZqJeHp9eSZqKpTP6VpMWffT/cwvHfdtrnixk=; b=gxwXAwPcZD/8OV12/GYpWppWG9KnrACxLJ5Yl8TbfI1YV7jMyFhEiNQpT3AUsJHOmY IzzxClzppSV3nNUX/TChLoJ1JBkDtViPw5Ta09DhEQSbc0Tu8C8O8Vdas6ro5b3xcwF0 tJI3QwQNoIBJQQ/wegVQz3HDMX8UiTQR9XERS0TXbq4ajYhloR7QpNJ3+SG8LDXQEipg l7njygVk361HkCihu3c5h/4MjLbJpOGONRcLgd8y3FoFgbVsXxT4CipqqtQCjZTLYo43 +iFZ7nH9hHWw3mAhqiA+1tPGmVhYLYzYf1//vfeFetJZmXapduABFi890b/wLkxg2seR /EAQ== X-Gm-Message-State: AOAM530+SwTsi4l0yHL1jqEKGleUpvBkDLvGqNFSDOcbC9duHcCLR6mL aWQTDP8Z1qS4ZmEPv9DPtlxAb+IrtkHX0PSkRa8= X-Google-Smtp-Source: ABdhPJwJevNLB+oYhXtd2ULd+UH5FKiGS/oc+AB36XsW287DmTXKj8UzsJ1+fZ/rW/oK8ADNSbwGUEdUmslnqq/DbGA= X-Received: by 2002:a17:902:eec4:: with SMTP id h4mr2976110plb.241.1598367817354; Tue, 25 Aug 2020 08:03:37 -0700 (PDT) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> <87imd6x5to.fsf@HIDDEN> In-Reply-To: <87imd6x5to.fsf@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Tue, 25 Aug 2020 17:03:26 +0200 Message-ID: <CA+Jv8O1uj5XrWk6PnO4UCwjBPxmfV+4QM_+uosP71POG6vkyTg@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="000000000000f952be05adb5015a" X-Spam-Score: 0.5 (/) X-Debbugs-Envelope-To: 42920 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.5 (/) --000000000000f952be05adb5015a Content-Type: text/plain; charset="UTF-8" Hi Ricardo, On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <rekado@HIDDEN> wrote: > > > The problem with the prompt arises from step 4), because 'conda' has bash > > as interpreter, and "non-interactive bashes go out of their way to unset > > PS1": > > > https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1 > > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html > > Good sleuthing! > > > So .conda.real never gets the PS1 variable and it disappears. I did some more experiments, and forcing the wrapper script to start in interactive mode solves the problem. `conda init` adds some things to `.bashrc`, in particular it `eval`s the output from `conda shell.bash hook`, which creates the `conda` bash function (and associated functions). The output from `conda shell.bash hook` seems to be based on `/etc/profile.d/conda.sh`: https://github.com/conda/conda/blob/master/conda/shell/etc/profile.d/conda.sh As in, it prefixes some environment variables and appends the activation of the base environment. Now if we replace all 5 occurances of "$CONDA_EXE" $_CE_M $_CE_CONDA in that file with bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA then everything works as expected. The -i is to enable interactive mode, preventing PS1 from being eaten. --norc is necessary to not source .bashrc. There are two occurences of "$CONDA_EXE" that should not be replaced, hence adding the CE variables. Would editing files like that be possible in a guix package script? It seems that it is only a simple sed replace on a single file. It is a bit hackish, because it adds knowledge to the package that a) there is a wrapper script and b) it is in bash. I have only experimented with it by copying the output off `conda shell.bash hook` to a file in my home directory and editing that. Maybe I can try to update the package too. Other options: - Use some other sh than bash, one that does not eat PS1, (e.g. dash) as wrapper script. I just verified that *all* wrappers on my machine are bash. However, some are using bash-minimal, so that means that there is a choice, so maybe switching shells is possible? - Somehow let conda work with another variable than PS1. Seems more complicated. Then what is left is updating `conda init` such that - it doesn't complain when it cannot edit files - it only uses paths in ~/.guix-profile but this is not essential to get conda to work. Cheers, Hugo --000000000000f952be05adb5015a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hi Ricardo,<br></div><br><div><div dir=3D"ltr" class= =3D"gmail_attr">On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <<a href=3D= "mailto:rekado@HIDDEN">rekado@HIDDEN</a>> wrote:<br></div><blo= ckquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left= :1px solid rgb(204,204,204);padding-left:1ex"><br> > The problem with the prompt arises from step 4), because 'conda= 9; has bash<br> > as interpreter, and "non-interactive bashes go out of their way t= o unset<br> > PS1":<br> > <a href=3D"https://superuser.com/questions/663069/why-does-subshell-no= t-inherit-exported-variable-ps1" rel=3D"noreferrer" target=3D"_blank">https= ://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-va= riable-ps1</a><br> > <a href=3D"https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html" rel=3D= "noreferrer" target=3D"_blank">https://tldp.org/HOWTO/Bash-Prompt-HOWTO/set= ps.html</a><br> <br> Good sleuthing!<br> <br> > So .conda.real never gets the PS1 variable and it disappears.</blockqu= ote><div><br></div><div>I did some more experiments, and forcing the wrappe= r script to start in interactive mode solves the problem.</div><div><br></d= iv>`conda init` adds some things to `.bashrc`, in particular it `eval`s the= output from `conda shell.bash hook`, which creates the `conda` bash functi= on (and associated functions).</div><div><br></div><div>The output from `co= nda shell.bash hook` seems to be based on `/etc/profile.d/conda.sh`:<br></d= iv><div><a href=3D"https://github.com/conda/conda/blob/master/conda/shell/e= tc/profile.d/conda.sh">https://github.com/conda/conda/blob/master/conda/she= ll/etc/profile.d/conda.sh</a></div><div>As in, it prefixes some environment= variables and appends the activation of the base environment.</div><div><b= r></div><div>Now if we replace all 5 occurances of</div><div>"$CONDA_E= XE" $_CE_M $_CE_CONDA</div><div>in that file with</div><div>bash --nor= c -i "$CONDA_EXE" $_CE_M $_CE_CONDA</div><div>then everything wor= ks as expected.</div><div><br></div><div>The -i is to enable interactive mo= de, preventing PS1 from being eaten. --norc is necessary to not source .bas= hrc.<br></div><div>There are two occurences of "$CONDA_EXE" that = should not be replaced, hence adding the CE variables.</div><div><br></div>= <div>Would editing files like that be possible in a guix package script?</d= iv><div><br></div><div><div>It seems that it is only a simple sed replace o= n a single file. It is a bit hackish, because it adds knowledge to the pack= age that a) there is a wrapper script and b) it is in bash.</div></div><div= ><br></div><div>I have only experimented with it by copying the output off = `conda shell.bash hook` to a file in my home directory and editing that. Ma= ybe I can try to update the package too.<br></div><div><br></div><div>Other= options:</div><div>- Use some other sh than bash, one that does not eat PS= 1, (e.g. dash) as wrapper script. I just verified that *all* wrappers on my= machine are bash. However, some are using bash-minimal, so that means that= there is a choice, so maybe switching shells is possible?</div><div>- Some= how let conda work with another variable than PS1. Seems more complicated.<= /div><div><br></div><div>Then what is left is updating `conda init` such th= at</div><div>- it doesn't complain when it cannot edit files</div><div>= - it only uses paths in ~/.guix-profile</div><div>but this is not essential= to get conda to work.<br></div><div><br></div><div>Cheers,</div><div>Hugo<= /div><div><br></div></div> --000000000000f952be05adb5015a--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at submit) by debbugs.gnu.org; 25 Aug 2020 15:03:58 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Aug 25 11:03:58 2020 Received: from localhost ([127.0.0.1]:35674 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1kAaUQ-0004z6-D2 for submit <at> debbugs.gnu.org; Tue, 25 Aug 2020 11:03:58 -0400 Received: from lists.gnu.org ([209.51.188.17]:52386) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1kAaUO-0004yx-0J for submit <at> debbugs.gnu.org; Tue, 25 Aug 2020 11:03:56 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54210) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1kAaUN-0007AO-QY for bug-guix@HIDDEN; Tue, 25 Aug 2020 11:03:55 -0400 Received: from mail-pg1-f179.google.com ([209.85.215.179]:34526) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1kAaU7-0002mt-Mp for bug-guix@HIDDEN; Tue, 25 Aug 2020 11:03:55 -0400 Received: by mail-pg1-f179.google.com with SMTP id i10so7019958pgk.1 for <bug-guix@HIDDEN>; Tue, 25 Aug 2020 08:03:38 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=vuwKIn4ZqJeHp9eSZqKpTP6VpMWffT/cwvHfdtrnixk=; b=N/IBRpJ27/pNmdTvCPLgr8MchSrC7X1dLQWQziEGa4jV72vlDo9bMOHLgyZDyTvcAy UByvngxlrbzNxZz5IPhvZZaKGlFQXzBHNA8t5dNvqaQAxSKzNiy95+Qyq9E7kN2fsXaQ ufHZnDZxbsOglXoQchWucTigAk6wv2r126hGcppAzr3eEsfcGrhiue9P51zlnoo7hTmf 0tO4i8BgK5NbAmaYQl2fTMEWsUDc8VlMhYph9eZHqA8grDqJL+3cf6Mdz+w3hIiK6EYY liH/7wffeDhRz/zozknJHD0++QKL5QaU7SoAU1sRWEWzkVyFRNuCbqrkLuwlC/QfNTgW 43zA== X-Gm-Message-State: AOAM531hR9XptXSupdbILs1SDgF+EWhO5DkE9GYzY26Lqv47/HZ1U6it CRR7SuuVSxz4yJRZwn1rkoimnFOGqwoSh2ANW1hQEmkrv4pV7w== X-Google-Smtp-Source: ABdhPJwJevNLB+oYhXtd2ULd+UH5FKiGS/oc+AB36XsW287DmTXKj8UzsJ1+fZ/rW/oK8ADNSbwGUEdUmslnqq/DbGA= X-Received: by 2002:a17:902:eec4:: with SMTP id h4mr2976110plb.241.1598367817354; Tue, 25 Aug 2020 08:03:37 -0700 (PDT) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> <87imd6x5to.fsf@HIDDEN> In-Reply-To: <87imd6x5to.fsf@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Tue, 25 Aug 2020 17:03:26 +0200 Message-ID: <CA+Jv8O1uj5XrWk6PnO4UCwjBPxmfV+4QM_+uosP71POG6vkyTg@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="000000000000f952be05adb5015a" Received-SPF: pass client-ip=209.85.215.179; envelope-from=blackshift@HIDDEN; helo=mail-pg1-f179.google.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/25 11:03:37 X-ACL-Warn: Detected OS = Linux 2.2.x-3.x [generic] [fuzzy] X-Spam_score_int: -13 X-Spam_score: -1.4 X-Spam_bar: - X-Spam_report: (-1.4 / 5.0 requ) BAYES_00=-1.9, FREEMAIL_FORGED_FROMDOMAIN=0.248, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=0.248, HTML_MESSAGE=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.8 (/) X-Debbugs-Envelope-To: submit Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.8 (-) --000000000000f952be05adb5015a Content-Type: text/plain; charset="UTF-8" Hi Ricardo, On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <rekado@HIDDEN> wrote: > > > The problem with the prompt arises from step 4), because 'conda' has bash > > as interpreter, and "non-interactive bashes go out of their way to unset > > PS1": > > > https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1 > > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html > > Good sleuthing! > > > So .conda.real never gets the PS1 variable and it disappears. I did some more experiments, and forcing the wrapper script to start in interactive mode solves the problem. `conda init` adds some things to `.bashrc`, in particular it `eval`s the output from `conda shell.bash hook`, which creates the `conda` bash function (and associated functions). The output from `conda shell.bash hook` seems to be based on `/etc/profile.d/conda.sh`: https://github.com/conda/conda/blob/master/conda/shell/etc/profile.d/conda.sh As in, it prefixes some environment variables and appends the activation of the base environment. Now if we replace all 5 occurances of "$CONDA_EXE" $_CE_M $_CE_CONDA in that file with bash --norc -i "$CONDA_EXE" $_CE_M $_CE_CONDA then everything works as expected. The -i is to enable interactive mode, preventing PS1 from being eaten. --norc is necessary to not source .bashrc. There are two occurences of "$CONDA_EXE" that should not be replaced, hence adding the CE variables. Would editing files like that be possible in a guix package script? It seems that it is only a simple sed replace on a single file. It is a bit hackish, because it adds knowledge to the package that a) there is a wrapper script and b) it is in bash. I have only experimented with it by copying the output off `conda shell.bash hook` to a file in my home directory and editing that. Maybe I can try to update the package too. Other options: - Use some other sh than bash, one that does not eat PS1, (e.g. dash) as wrapper script. I just verified that *all* wrappers on my machine are bash. However, some are using bash-minimal, so that means that there is a choice, so maybe switching shells is possible? - Somehow let conda work with another variable than PS1. Seems more complicated. Then what is left is updating `conda init` such that - it doesn't complain when it cannot edit files - it only uses paths in ~/.guix-profile but this is not essential to get conda to work. Cheers, Hugo --000000000000f952be05adb5015a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hi Ricardo,<br></div><br><div><div dir=3D"ltr" class= =3D"gmail_attr">On Tue, 25 Aug 2020 at 14:35, Ricardo Wurmus <<a href=3D= "mailto:rekado@HIDDEN">rekado@HIDDEN</a>> wrote:<br></div><blo= ckquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left= :1px solid rgb(204,204,204);padding-left:1ex"><br> > The problem with the prompt arises from step 4), because 'conda= 9; has bash<br> > as interpreter, and "non-interactive bashes go out of their way t= o unset<br> > PS1":<br> > <a href=3D"https://superuser.com/questions/663069/why-does-subshell-no= t-inherit-exported-variable-ps1" rel=3D"noreferrer" target=3D"_blank">https= ://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-va= riable-ps1</a><br> > <a href=3D"https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html" rel=3D= "noreferrer" target=3D"_blank">https://tldp.org/HOWTO/Bash-Prompt-HOWTO/set= ps.html</a><br> <br> Good sleuthing!<br> <br> > So .conda.real never gets the PS1 variable and it disappears.</blockqu= ote><div><br></div><div>I did some more experiments, and forcing the wrappe= r script to start in interactive mode solves the problem.</div><div><br></d= iv>`conda init` adds some things to `.bashrc`, in particular it `eval`s the= output from `conda shell.bash hook`, which creates the `conda` bash functi= on (and associated functions).</div><div><br></div><div>The output from `co= nda shell.bash hook` seems to be based on `/etc/profile.d/conda.sh`:<br></d= iv><div><a href=3D"https://github.com/conda/conda/blob/master/conda/shell/e= tc/profile.d/conda.sh">https://github.com/conda/conda/blob/master/conda/she= ll/etc/profile.d/conda.sh</a></div><div>As in, it prefixes some environment= variables and appends the activation of the base environment.</div><div><b= r></div><div>Now if we replace all 5 occurances of</div><div>"$CONDA_E= XE" $_CE_M $_CE_CONDA</div><div>in that file with</div><div>bash --nor= c -i "$CONDA_EXE" $_CE_M $_CE_CONDA</div><div>then everything wor= ks as expected.</div><div><br></div><div>The -i is to enable interactive mo= de, preventing PS1 from being eaten. --norc is necessary to not source .bas= hrc.<br></div><div>There are two occurences of "$CONDA_EXE" that = should not be replaced, hence adding the CE variables.</div><div><br></div>= <div>Would editing files like that be possible in a guix package script?</d= iv><div><br></div><div><div>It seems that it is only a simple sed replace o= n a single file. It is a bit hackish, because it adds knowledge to the pack= age that a) there is a wrapper script and b) it is in bash.</div></div><div= ><br></div><div>I have only experimented with it by copying the output off = `conda shell.bash hook` to a file in my home directory and editing that. Ma= ybe I can try to update the package too.<br></div><div><br></div><div>Other= options:</div><div>- Use some other sh than bash, one that does not eat PS= 1, (e.g. dash) as wrapper script. I just verified that *all* wrappers on my= machine are bash. However, some are using bash-minimal, so that means that= there is a choice, so maybe switching shells is possible?</div><div>- Some= how let conda work with another variable than PS1. Seems more complicated.<= /div><div><br></div><div>Then what is left is updating `conda init` such th= at</div><div>- it doesn't complain when it cannot edit files</div><div>= - it only uses paths in ~/.guix-profile</div><div>but this is not essential= to get conda to work.<br></div><div><br></div><div>Cheers,</div><div>Hugo<= /div><div><br></div></div> --000000000000f952be05adb5015a--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 25 Aug 2020 12:34:28 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Aug 25 08:34:28 2020 Received: from localhost ([127.0.0.1]:60642 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1kAY9j-0001d1-QT for submit <at> debbugs.gnu.org; Tue, 25 Aug 2020 08:34:28 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21196) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1kAY9h-0001cm-Ta for 42920 <at> debbugs.gnu.org; Tue, 25 Aug 2020 08:34:26 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1598358858; cv=none; d=zohomail.com; s=zohoarc; b=UaTiRjw764EIs1SQV4kL4uSwOOA+tixbvdzcJPk8OEWwyymHW1DSqCietxtiS/7Ex5iX2uQf5n/Frwebd1J0QKkya1msIyO9HR6IxYVBrM88IfWFAufSKKFkYcNEJHJTVowlfqye/0t2qhxs+OEkiLkYJMCxRwySKaLMTYrp6/E= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1598358858; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=jv7a5d8OB+bLMi58WLlJZ5WC8HZq5AiNKSNsAfU/rdQ=; b=ldaK/9lEVSiO2eqVAYzna7cTUmJo8XslTOsVSftfG6ONhUvlIENCvM6f5P0gTrhSKb/1VqxgC21OJquoIl4LzWyDsiNqHmOWT3PeeWZOEG7KNHuoaFCJLxSwkPXrRY5V24b1nY03JQO1SLnn50E9TbCyvxxPOiT+EN890ANzDow= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1598358858; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=jv7a5d8OB+bLMi58WLlJZ5WC8HZq5AiNKSNsAfU/rdQ=; b=Y14Lk5Go0qkLBTu1zNPQAI5QQaVuDuDYvd4HXk+AtKOYLNBueqTA943BlrLn4rp9 EgauJ9yqbYzwYo2afx1ebqnsFa1T/e+HYemsJN15vC0Y9cRSZcfk326gc3YphI5yr9D 9sCUFnVm8fxKLJkVWXrNo/mWDituTJAi3NhQKkUM= Received: from localhost (p54ad4c14.dip0.t-ipconnect.de [84.173.76.20]) by mx.zohomail.com with SMTPS id 1598358854650721.6492113191758; Tue, 25 Aug 2020 05:34:14 -0700 (PDT) References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> User-agent: mu4e 1.4.10; emacs 26.3 From: Ricardo Wurmus <rekado@HIDDEN> To: Hugo Buddelmeijer <hugo@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments In-reply-to: <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 25 Aug 2020 14:34:11 +0200 Message-ID: <87imd6x5to.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 42920 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hi Hugo, > The problem with the prompt arises from step 4), because 'conda' has bash > as interpreter, and "non-interactive bashes go out of their way to unset > PS1": > https://superuser.com/questions/663069/why-does-subshell-not-inherit-expo= rted-variable-ps1 > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html Good sleuthing! > So .conda.real never gets the PS1 variable and it disappears. > > I don't really understand why there is a bash function, a conda bash scri= pt > and a .conda-real python script. That=E2=80=99s because we wrap application to ensure that they run with exp= ected environment variables. By default this wrapper is implemented as a Bash script, but we also have =E2=80=9Cwrap-script=E2=80=9D, which turns scripts= using =E2=80=9C#=E2=80=9D as a comment character into polyglottal Guile scripts, setting variables with Guile and then reexecuting themselves with the actual interpreter. Not sure if that would help here. (There also have been reports about =E2=80=9Cwrap-script=E2=80=9D being bug= gy, but I don=E2=80=99t recall any details.) --=20 Ricardo
bug-guix@HIDDEN
:bug#42920
; Package guix
.
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i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=jv7a5d8OB+bLMi58WLlJZ5WC8HZq5AiNKSNsAfU/rdQ=; b=Y14Lk5Go0qkLBTu1zNPQAI5QQaVuDuDYvd4HXk+AtKOYLNBueqTA943BlrLn4rp9 EgauJ9yqbYzwYo2afx1ebqnsFa1T/e+HYemsJN15vC0Y9cRSZcfk326gc3YphI5yr9D 9sCUFnVm8fxKLJkVWXrNo/mWDituTJAi3NhQKkUM= Received: from localhost (p54ad4c14.dip0.t-ipconnect.de [84.173.76.20]) by mx.zohomail.com with SMTPS id 1598358854650721.6492113191758; Tue, 25 Aug 2020 05:34:14 -0700 (PDT) References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> User-agent: mu4e 1.4.10; emacs 26.3 From: Ricardo Wurmus <rekado@HIDDEN> To: Hugo Buddelmeijer <hugo@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments In-reply-to: <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 25 Aug 2020 14:34:11 +0200 Message-ID: <87imd6x5to.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Received-SPF: pass client-ip=136.143.188.51; envelope-from=rekado@HIDDEN; helo=sender4-of-o51.zoho.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/25 08:34:19 X-ACL-Warn: Detected OS = Linux 3.11 and newer [fuzzy] 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, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H2=-0.001, 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 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -2.3 (--) Hi Hugo, > The problem with the prompt arises from step 4), because 'conda' has bash > as interpreter, and "non-interactive bashes go out of their way to unset > PS1": > https://superuser.com/questions/663069/why-does-subshell-not-inherit-expo= rted-variable-ps1 > https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html Good sleuthing! > So .conda.real never gets the PS1 variable and it disappears. > > I don't really understand why there is a bash function, a conda bash scri= pt > and a .conda-real python script. That=E2=80=99s because we wrap application to ensure that they run with exp= ected environment variables. By default this wrapper is implemented as a Bash script, but we also have =E2=80=9Cwrap-script=E2=80=9D, which turns scripts= using =E2=80=9C#=E2=80=9D as a comment character into polyglottal Guile scripts, setting variables with Guile and then reexecuting themselves with the actual interpreter. Not sure if that would help here. (There also have been reports about =E2=80=9Cwrap-script=E2=80=9D being bug= gy, but I don=E2=80=99t recall any details.) --=20 Ricardo
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 23 Aug 2020 19:26:58 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Aug 23 15:26:58 2020 Received: from localhost ([127.0.0.1]:55154 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k9vdq-0005AE-4i for submit <at> debbugs.gnu.org; Sun, 23 Aug 2020 15:26:58 -0400 Received: from mail-pj1-f48.google.com ([209.85.216.48]:40906) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1k9vdo-00059s-8Q for 42920 <at> debbugs.gnu.org; Sun, 23 Aug 2020 15:26:56 -0400 Received: by mail-pj1-f48.google.com with SMTP id d4so3053982pjx.5 for <42920 <at> debbugs.gnu.org>; Sun, 23 Aug 2020 12:26:56 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=sJUq2M0TUo575Kc0WiPrzMKym4LaG3lqNqxH6LmdSY8=; b=czjDMEiRruPrT09TRsmlG2Sqwaj2B9K2UUFZvxxk9jG53DjE/xfBsyuf+DLkWrZyWV CBeFSqqgtMYpWMml/BLq0212zXOoeRInY4vf67/pe1n7CEpvvCBoThR6eS+7BAPbE2Eq hjiJshktHu7uGKYH3dgeYTvITCNG7X22RBZJHa3J7tx47lap98LCYgzbo4AdIfHPf3dI RQlqodFpVILPtU6BqbZJ4Ofb9Nj6m3+nbtrNhPxy1R10gC5eQxETjFyOZlPx2VtETnX4 c0pOWQfYCgyBGGxxdvHoqh+y7h8Nfo7pvCEgQ/qyu4KvJLdbZRz1U6oGF69rR2LDsb8b aLfA== X-Gm-Message-State: AOAM531y2tiGOYNXPLEatkkGXep1qvJKEztfjAUpvArFTI+YNOuP3Cp9 W1lLUwe3vkhg8pjKC3ZSy1COCjP/arWyKWLhM7A= X-Google-Smtp-Source: ABdhPJz3tz4XJRo+zXjqUyBDn83Gisp0RbQ+UEvDOPhiahNorN1QBUNvKisdEUOV9nyVWKxyYT/aTyelp+priL1nAKI= X-Received: by 2002:a17:902:523:: with SMTP id 32mr1532046plf.176.1598210810265; Sun, 23 Aug 2020 12:26:50 -0700 (PDT) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> In-Reply-To: <87364gy7tw.fsf@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Sun, 23 Aug 2020 21:26:39 +0200 Message-ID: <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="0000000000009f441605ad907366" X-Spam-Score: 0.5 (/) X-Debbugs-Envelope-To: 42920 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.5 (/) --0000000000009f441605ad907366 Content-Type: text/plain; charset="UTF-8" Just sharing a bit of more info about why the conda prompt breaks. On Fri, 21 Aug 2020 at 05:52, Ricardo Wurmus <rekado@HIDDEN> wrote: > > Hugo Buddelmeijer <hugo@HIDDEN> writes: > > > 2. The prompt is not set correctly, as in, what should happen is that the > > current conda environment is added to the prompt. Instead, the prompt is > > replaced entirely by the environment. This shouldn't be too hard to fix > > manually though. > > Weird! Is this something Conda does wrong because it assumes too much > about the existing prompt? > This is what happens, reducing the files to the essence: 1) .bashrc runs __conda_setup="$('/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" eval "$__conda_setup" 2) __conda_setup runs __conda_activate() { ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix "$cmd" "$@")" || \return $? \eval "$ask_conda" } conda activate base 3) ask_conda will contain the new PS1 definition. The command ran to create ask_conda is PS1="\u@\h \w\$" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda" shell.posix "activate" "base" 4) conda runs #!/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash export PYTHONPATH="/gnu/store....." exec -a "$0" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.conda-real" "$@" 5) .conda.real generates the prompt in Python: from conda.cli import main sys.exit(main()) 6) .conda.real outputs PS1='(base) ' export PATH='... The problem with the prompt arises from step 4), because 'conda' has bash as interpreter, and "non-interactive bashes go out of their way to unset PS1": https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1 https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html So .conda.real never gets the PS1 variable and it disappears. I don't really understand why there is a bash function, a conda bash script and a .conda-real python script. My local miniconda 4.8.3 installation on an Ubuntu machine (in my home directory) does not have a ".conda-real": "conda" directly is the Python script, so everything works. Maybe more later. Hugo > -- > Ricardo > --0000000000009f441605ad907366 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Just sharing a bit of more info about why the conda p= rompt breaks.</div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D= "gmail_attr">On Fri, 21 Aug 2020 at 05:52, Ricardo Wurmus <<a href=3D"ma= ilto:rekado@HIDDEN">rekado@HIDDEN</a>> wrote:<br></div><blockq= uote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1p= x solid rgb(204,204,204);padding-left:1ex"><br> Hugo Buddelmeijer <<a href=3D"mailto:hugo@HIDDEN" target=3D"_bl= ank">hugo@HIDDEN</a>> writes:<br> <br> > 2. The prompt is not set correctly, as in, what should happen is that = the<br> > current conda environment is added to the prompt. Instead, the prompt = is<br> > replaced entirely by the environment. This shouldn't be too hard t= o fix<br> > manually though.<br> <br> Weird!=C2=A0 Is this something Conda does wrong because it assumes too much= <br> about the existing prompt?<br></blockquote><div><br></div><div>This is what= happens, reducing the files to the essence:</div><div><br></div><div>1) .b= ashrc runs<br></div><div><br></div><div>__conda_setup=3D"$('/gnu/s= tore/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda' 'shell= .bash' 'hook' 2> /dev/null)"<br>eval "$__conda_set= up"<br></div><div><br></div><div>2) __conda_setup runs<br></div><div><= br></div><div>__conda_activate() {<br>=C2=A0 =C2=A0 ask_conda=3D"$(PS1= =3D"$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix &q= uot;$cmd" "$@")" || \return $?<br> =C2=A0 =C2=A0 \eval = "$ask_conda"<br>}<br></div><div>conda activate base<br></div><div= ><br></div><div>3) ask_conda will contain the new PS1 definition. The comma= nd ran to create ask_conda=C2=A0 is<br></div><div><br></div><div>PS1=3D&quo= t;\u@\h \w\$" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-= 4.8.3/bin/conda" =C2=A0 shell.posix "activate" "base&qu= ot;</div><div><br></div><div>4) conda runs<br></div><div><br></div><div>#!/= gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash</di= v><div>export PYTHONPATH=3D"/gnu/store....."</div><div>exec -a &q= uot;$0" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/= bin/.conda-real" "$@"<br></div><div><br></div><div>5) .conda= .real generates the prompt in Python:<br></div><div><br></div><div>from con= da.cli import main<br>sys.exit(main())<br></div><div><br></div><div>6) .con= da.real outputs</div><div>PS1=3D'(base) '<br>export PATH=3D'...= </div><div><br></div><div>The problem with the prompt arises from step 4), = because 'conda' has bash as interpreter, and "non-interactive = bashes go out of their way to unset PS1":</div><div><a href=3D"https:/= /superuser.com/questions/663069/why-does-subshell-not-inherit-exported-vari= able-ps1">https://superuser.com/questions/663069/why-does-subshell-not-inhe= rit-exported-variable-ps1</a></div><div><a href=3D"https://tldp.org/HOWTO/B= ash-Prompt-HOWTO/setps.html">https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps= .html</a></div><div><br></div><div>So .conda.real never gets the PS1 variab= le and it disappears.</div><div><br></div><div>I don't really understan= d why there is a bash function, a conda bash script and a .conda-real pytho= n script.</div><div><br></div></div><div class=3D"gmail_quote"><div>My loca= l miniconda 4.8.3 installation on an Ubuntu machine (in my home directory) = does not have a ".conda-real": "conda" directly is the = Python script, so everything works.<br></div><div>=C2=A0</div><div> Maybe m= ore later.</div><div><br></div><div>Hugo</div><div><br></div><div><br></div= ><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border= -left:1px solid rgb(204,204,204);padding-left:1ex"> <br> -- <br> Ricardo<br> </blockquote></div></div> --0000000000009f441605ad907366--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at submit) by debbugs.gnu.org; 23 Aug 2020 19:26:58 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Aug 23 15:26:58 2020 Received: from localhost ([127.0.0.1]:55152 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k9vdp-0005AC-NV for submit <at> debbugs.gnu.org; Sun, 23 Aug 2020 15:26:58 -0400 Received: from lists.gnu.org ([209.51.188.17]:41072) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1k9vdn-00059y-KF for submit <at> debbugs.gnu.org; Sun, 23 Aug 2020 15:26:56 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35752) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1k9vdn-0003v2-Dr for bug-guix@HIDDEN; Sun, 23 Aug 2020 15:26:55 -0400 Received: from mail-pj1-f54.google.com ([209.85.216.54]:33096) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1k9vdk-0003qq-MS for bug-guix@HIDDEN; Sun, 23 Aug 2020 15:26:55 -0400 Received: by mail-pj1-f54.google.com with SMTP id q93so2421419pjq.0 for <bug-guix@HIDDEN>; Sun, 23 Aug 2020 12:26:51 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=sJUq2M0TUo575Kc0WiPrzMKym4LaG3lqNqxH6LmdSY8=; b=uCubvFi5BlfKTcf1KPL//4Jtii4D3oyjReXZGE36DkMcaCalaevdbnfYZ+4Maecagq LEQ58KLx94xmLx4ziBwQq9CeSbVmWvnEPQYRsfgWb1LN6r0k9EVqkYmrRvtRonGDBqMT IBTDLUHNFJdDeRVfMl8cePTjpqW5AvjU50oKO/6RSiHfpuSnwf6lZ2cdKd4KxOlzWtm0 5QMBGsvuMAAHPoBfZqI6Sl2ri3ah09IZsSnx9eeV8jR34xuulTxZzviRQEIrI2m3ovLx F4bQfwyxm0m/g8XePP7Q2U8rBr+c828i5p2ljflfqdLkO3gIA1xltDcMZYhbDinrxPX/ UP4A== X-Gm-Message-State: AOAM532LQ6cy9uBBNyPVsrGzoJA+Goe33Psh12rtWAy+JXZcMBqWb+5K GDpKuF4KryQquOWWAHkGGTGIZaKOwx60ShWo7xw= X-Google-Smtp-Source: ABdhPJz3tz4XJRo+zXjqUyBDn83Gisp0RbQ+UEvDOPhiahNorN1QBUNvKisdEUOV9nyVWKxyYT/aTyelp+priL1nAKI= X-Received: by 2002:a17:902:523:: with SMTP id 32mr1532046plf.176.1598210810265; Sun, 23 Aug 2020 12:26:50 -0700 (PDT) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> <87364gy7tw.fsf@HIDDEN> In-Reply-To: <87364gy7tw.fsf@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Sun, 23 Aug 2020 21:26:39 +0200 Message-ID: <CA+Jv8O1NFPMZ+bcDNmzLhNq_KGjqsR67g_c-EOHEpfg47f070A@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="0000000000009f441605ad907366" Received-SPF: pass client-ip=209.85.216.54; envelope-from=blackshift@HIDDEN; helo=mail-pj1-f54.google.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/23 15:26:50 X-ACL-Warn: Detected OS = Linux 2.2.x-3.x [generic] [fuzzy] X-Spam_score_int: -13 X-Spam_score: -1.4 X-Spam_bar: - X-Spam_report: (-1.4 / 5.0 requ) BAYES_00=-1.9, FREEMAIL_FORGED_FROMDOMAIN=0.25, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=0.25, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H3=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.8 (/) X-Debbugs-Envelope-To: submit Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.8 (-) --0000000000009f441605ad907366 Content-Type: text/plain; charset="UTF-8" Just sharing a bit of more info about why the conda prompt breaks. On Fri, 21 Aug 2020 at 05:52, Ricardo Wurmus <rekado@HIDDEN> wrote: > > Hugo Buddelmeijer <hugo@HIDDEN> writes: > > > 2. The prompt is not set correctly, as in, what should happen is that the > > current conda environment is added to the prompt. Instead, the prompt is > > replaced entirely by the environment. This shouldn't be too hard to fix > > manually though. > > Weird! Is this something Conda does wrong because it assumes too much > about the existing prompt? > This is what happens, reducing the files to the essence: 1) .bashrc runs __conda_setup="$('/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" eval "$__conda_setup" 2) __conda_setup runs __conda_activate() { ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix "$cmd" "$@")" || \return $? \eval "$ask_conda" } conda activate base 3) ask_conda will contain the new PS1 definition. The command ran to create ask_conda is PS1="\u@\h \w\$" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda" shell.posix "activate" "base" 4) conda runs #!/gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash export PYTHONPATH="/gnu/store....." exec -a "$0" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.conda-real" "$@" 5) .conda.real generates the prompt in Python: from conda.cli import main sys.exit(main()) 6) .conda.real outputs PS1='(base) ' export PATH='... The problem with the prompt arises from step 4), because 'conda' has bash as interpreter, and "non-interactive bashes go out of their way to unset PS1": https://superuser.com/questions/663069/why-does-subshell-not-inherit-exported-variable-ps1 https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps.html So .conda.real never gets the PS1 variable and it disappears. I don't really understand why there is a bash function, a conda bash script and a .conda-real python script. My local miniconda 4.8.3 installation on an Ubuntu machine (in my home directory) does not have a ".conda-real": "conda" directly is the Python script, so everything works. Maybe more later. Hugo > -- > Ricardo > --0000000000009f441605ad907366 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Just sharing a bit of more info about why the conda p= rompt breaks.</div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D= "gmail_attr">On Fri, 21 Aug 2020 at 05:52, Ricardo Wurmus <<a href=3D"ma= ilto:rekado@HIDDEN">rekado@HIDDEN</a>> wrote:<br></div><blockq= uote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1p= x solid rgb(204,204,204);padding-left:1ex"><br> Hugo Buddelmeijer <<a href=3D"mailto:hugo@HIDDEN" target=3D"_bl= ank">hugo@HIDDEN</a>> writes:<br> <br> > 2. The prompt is not set correctly, as in, what should happen is that = the<br> > current conda environment is added to the prompt. Instead, the prompt = is<br> > replaced entirely by the environment. This shouldn't be too hard t= o fix<br> > manually though.<br> <br> Weird!=C2=A0 Is this something Conda does wrong because it assumes too much= <br> about the existing prompt?<br></blockquote><div><br></div><div>This is what= happens, reducing the files to the essence:</div><div><br></div><div>1) .b= ashrc runs<br></div><div><br></div><div>__conda_setup=3D"$('/gnu/s= tore/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda' 'shell= .bash' 'hook' 2> /dev/null)"<br>eval "$__conda_set= up"<br></div><div><br></div><div>2) __conda_setup runs<br></div><div><= br></div><div>__conda_activate() {<br>=C2=A0 =C2=A0 ask_conda=3D"$(PS1= =3D"$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix &q= uot;$cmd" "$@")" || \return $?<br> =C2=A0 =C2=A0 \eval = "$ask_conda"<br>}<br></div><div>conda activate base<br></div><div= ><br></div><div>3) ask_conda will contain the new PS1 definition. The comma= nd ran to create ask_conda=C2=A0 is<br></div><div><br></div><div>PS1=3D&quo= t;\u@\h \w\$" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-= 4.8.3/bin/conda" =C2=A0 shell.posix "activate" "base&qu= ot;</div><div><br></div><div>4) conda runs<br></div><div><br></div><div>#!/= gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16/bin/bash</di= v><div>export PYTHONPATH=3D"/gnu/store....."</div><div>exec -a &q= uot;$0" "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/= bin/.conda-real" "$@"<br></div><div><br></div><div>5) .conda= .real generates the prompt in Python:<br></div><div><br></div><div>from con= da.cli import main<br>sys.exit(main())<br></div><div><br></div><div>6) .con= da.real outputs</div><div>PS1=3D'(base) '<br>export PATH=3D'...= </div><div><br></div><div>The problem with the prompt arises from step 4), = because 'conda' has bash as interpreter, and "non-interactive = bashes go out of their way to unset PS1":</div><div><a href=3D"https:/= /superuser.com/questions/663069/why-does-subshell-not-inherit-exported-vari= able-ps1">https://superuser.com/questions/663069/why-does-subshell-not-inhe= rit-exported-variable-ps1</a></div><div><a href=3D"https://tldp.org/HOWTO/B= ash-Prompt-HOWTO/setps.html">https://tldp.org/HOWTO/Bash-Prompt-HOWTO/setps= .html</a></div><div><br></div><div>So .conda.real never gets the PS1 variab= le and it disappears.</div><div><br></div><div>I don't really understan= d why there is a bash function, a conda bash script and a .conda-real pytho= n script.</div><div><br></div></div><div class=3D"gmail_quote"><div>My loca= l miniconda 4.8.3 installation on an Ubuntu machine (in my home directory) = does not have a ".conda-real": "conda" directly is the = Python script, so everything works.<br></div><div>=C2=A0</div><div> Maybe m= ore later.</div><div><br></div><div>Hugo</div><div><br></div><div><br></div= ><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border= -left:1px solid rgb(204,204,204);padding-left:1ex"> <br> -- <br> Ricardo<br> </blockquote></div></div> --0000000000009f441605ad907366--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 21 Aug 2020 03:52:26 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Aug 20 23:52:26 2020 Received: from localhost ([127.0.0.1]:44683 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k8y6M-0003jK-5w for submit <at> debbugs.gnu.org; Thu, 20 Aug 2020 23:52:26 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21170) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1k8y6K-0003jB-Hn for 42920 <at> debbugs.gnu.org; Thu, 20 Aug 2020 23:52:25 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1597981926; cv=none; d=zohomail.com; s=zohoarc; b=jD4FHdJ1rp3r04bZ25IUTKJOFMw4YacVhmCiKpuyzDsOhboWHaluelSs+ACGrFzY1qipqqeKooMdRx+5Mfs3zfBSz8H08FAQy7JCytJ2TrI5cM8Xw6euWNU/jRxun+8vtK1bU3OvMi8p6XNFxfS9V0vqCtdIF2bZUIaJntc7pms= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1597981926; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=X3DTWHiRZBsjWf/xAjNfiZehh94IZs7L4z98+433KmE=; b=GLXNIgi+XdqP7mdnLkYmfwkRhKGYZ3szL9o5eYuCfXk6e3PhmdcY3quSDRyBgCSKwEPbhXmVvAlVWNsP/tqpAf7dmDb+s/odO/LQJOl9zO+sLCo9++nsqVVskdtLtNZL9lCFYmwUPvBqRuHQrrs4jtoD51Lw0vHgAsjUX393BS0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1597981926; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=X3DTWHiRZBsjWf/xAjNfiZehh94IZs7L4z98+433KmE=; b=IFUve9DoKCCkmF049VNCq57pcdz7XtJaKBRxAl1kLppHk4L7nVihM7IhKxKbQ8A/ HopSWOSCKJBuXe8n0RvGlsoUkaTMkPZYKhooKhD4BfhI8Y4bMSEZoCXBTwTIklMwkpg kLA8rTQT133nH3wfP8y/s7ymWn2lhm3fHCol/7lA= Received: from localhost (p54ad4dde.dip0.t-ipconnect.de [84.173.77.222]) by mx.zohomail.com with SMTPS id 1597981919942706.723773905097; Thu, 20 Aug 2020 20:51:59 -0700 (PDT) References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> User-agent: mu4e 1.4.10; emacs 26.3 From: Ricardo Wurmus <rekado@HIDDEN> To: Hugo Buddelmeijer <hugo@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments In-reply-to: <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 21 Aug 2020 05:51:55 +0200 Message-ID: <87364gy7tw.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 42920 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hugo Buddelmeijer <hugo@HIDDEN> writes: > So there are three problems: > > 1. The PATHS in .bashrc should be to ~/.guix-profile/etc/profile.d/, not = to > /gnu/store directly. This is trivial to fix manually. Perhaps we can replace these locations with ${GUIX_PROFILE:-/gnu/store/=E2=80=A6} just as we do in our generated etc/pr= ofile file. > 2. The prompt is not set correctly, as in, what should happen is that the > current conda environment is added to the prompt. Instead, the prompt is > replaced entirely by the environment. This shouldn't be too hard to fix > manually though. Weird! Is this something Conda does wrong because it assumes too much about the existing prompt? > 3. The installed software does not have the proper interpreter set. This > can probably be fixed with patchelf, but now I'm wondering whether this is > the right approach, because that would be necessary for all packages > installed through conda. (Or is there a way to do that automatically? > Apparently just symlinking ld-linux-x86.so.2 into (from?) /lib64 also > works, but that feels like a very un-guixy hack.) There=E2=80=99s nothing we can do about this in a general fashion. Creatin= g a link from /lib64/ld-linux-x86-64.so.2 to the loader in the glibc package is indeed what is necessary on Guix System. If you don=E2=80=99t like to do this manually, you can use the extra-special-file service. > Sidenote, FWIW, there are also some problems with some of the scripts > installed in /gnu/store: > > hugo@alex ~$ > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda > -bash: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/python: bad > interpreter: No such file or directory > hugo@alex ~$ > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line > 3: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-rea= l: > Permission denied > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line > 3: exec: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-rea= l: > cannot execute: Permission denied > > It seems not necessary to actually use these scripts though. Would be good to fix them, though. The activate script may just need a chmod. Obviously, the bin/python thing is dead wrong =E2=80=94 I must have missed that instance of prefix confusion that litters the Conda code base. > Once we settle on a good way to approach this, where should we document > this? As in, if we want users to ignore the complaints from conda and > instead put something in their .bashrc manually, then that information > should be discoverable somehow. We shouldn=E2=80=99t need to document this at all; we should patch Conda to= do mostly the right thing. This involves limiting =E2=80=9Cconda init=E2=80= =9D to user-level changes. --=20 Ricardo
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at submit) by debbugs.gnu.org; 21 Aug 2020 03:52:31 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Aug 20 23:52:31 2020 Received: from localhost ([127.0.0.1]:44685 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k8y6Q-0003jZ-Q6 for submit <at> debbugs.gnu.org; Thu, 20 Aug 2020 23:52:31 -0400 Received: from lists.gnu.org ([209.51.188.17]:40090) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1k8y6M-0003jJ-0J for submit <at> debbugs.gnu.org; Thu, 20 Aug 2020 23:52:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41306) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <rekado@HIDDEN>) id 1k8y6I-0007BO-SV for bug-guix@HIDDEN; Thu, 20 Aug 2020 23:52:24 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21154) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_CBC_SHA1:256) (Exim 4.90_1) (envelope-from <rekado@HIDDEN>) id 1k8y68-000765-4U for bug-guix@HIDDEN; Thu, 20 Aug 2020 23:52:22 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1597981926; cv=none; d=zohomail.com; s=zohoarc; b=jD4FHdJ1rp3r04bZ25IUTKJOFMw4YacVhmCiKpuyzDsOhboWHaluelSs+ACGrFzY1qipqqeKooMdRx+5Mfs3zfBSz8H08FAQy7JCytJ2TrI5cM8Xw6euWNU/jRxun+8vtK1bU3OvMi8p6XNFxfS9V0vqCtdIF2bZUIaJntc7pms= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1597981926; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=X3DTWHiRZBsjWf/xAjNfiZehh94IZs7L4z98+433KmE=; b=GLXNIgi+XdqP7mdnLkYmfwkRhKGYZ3szL9o5eYuCfXk6e3PhmdcY3quSDRyBgCSKwEPbhXmVvAlVWNsP/tqpAf7dmDb+s/odO/LQJOl9zO+sLCo9++nsqVVskdtLtNZL9lCFYmwUPvBqRuHQrrs4jtoD51Lw0vHgAsjUX393BS0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1597981926; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=X3DTWHiRZBsjWf/xAjNfiZehh94IZs7L4z98+433KmE=; b=IFUve9DoKCCkmF049VNCq57pcdz7XtJaKBRxAl1kLppHk4L7nVihM7IhKxKbQ8A/ HopSWOSCKJBuXe8n0RvGlsoUkaTMkPZYKhooKhD4BfhI8Y4bMSEZoCXBTwTIklMwkpg kLA8rTQT133nH3wfP8y/s7ymWn2lhm3fHCol/7lA= Received: from localhost (p54ad4dde.dip0.t-ipconnect.de [84.173.77.222]) by mx.zohomail.com with SMTPS id 1597981919942706.723773905097; Thu, 20 Aug 2020 20:51:59 -0700 (PDT) References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> User-agent: mu4e 1.4.10; emacs 26.3 From: Ricardo Wurmus <rekado@HIDDEN> To: Hugo Buddelmeijer <hugo@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments In-reply-to: <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 21 Aug 2020 05:51:55 +0200 Message-ID: <87364gy7tw.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Received-SPF: pass client-ip=136.143.188.51; envelope-from=rekado@HIDDEN; helo=sender4-of-o51.zoho.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/20 23:52:07 X-ACL-Warn: Detected OS = Linux 3.11 and newer [fuzzy] X-Spam_score_int: -30 X-Spam_score: -3.1 X-Spam_bar: --- X-Spam_report: (-3.1 / 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, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H2=-1, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -2.3 (--) Hugo Buddelmeijer <hugo@HIDDEN> writes: > So there are three problems: > > 1. The PATHS in .bashrc should be to ~/.guix-profile/etc/profile.d/, not = to > /gnu/store directly. This is trivial to fix manually. Perhaps we can replace these locations with ${GUIX_PROFILE:-/gnu/store/=E2=80=A6} just as we do in our generated etc/pr= ofile file. > 2. The prompt is not set correctly, as in, what should happen is that the > current conda environment is added to the prompt. Instead, the prompt is > replaced entirely by the environment. This shouldn't be too hard to fix > manually though. Weird! Is this something Conda does wrong because it assumes too much about the existing prompt? > 3. The installed software does not have the proper interpreter set. This > can probably be fixed with patchelf, but now I'm wondering whether this is > the right approach, because that would be necessary for all packages > installed through conda. (Or is there a way to do that automatically? > Apparently just symlinking ld-linux-x86.so.2 into (from?) /lib64 also > works, but that feels like a very un-guixy hack.) There=E2=80=99s nothing we can do about this in a general fashion. Creatin= g a link from /lib64/ld-linux-x86-64.so.2 to the loader in the glibc package is indeed what is necessary on Guix System. If you don=E2=80=99t like to do this manually, you can use the extra-special-file service. > Sidenote, FWIW, there are also some problems with some of the scripts > installed in /gnu/store: > > hugo@alex ~$ > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda > -bash: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/python: bad > interpreter: No such file or directory > hugo@alex ~$ > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line > 3: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-rea= l: > Permission denied > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line > 3: exec: > /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-rea= l: > cannot execute: Permission denied > > It seems not necessary to actually use these scripts though. Would be good to fix them, though. The activate script may just need a chmod. Obviously, the bin/python thing is dead wrong =E2=80=94 I must have missed that instance of prefix confusion that litters the Conda code base. > Once we settle on a good way to approach this, where should we document > this? As in, if we want users to ignore the complaints from conda and > instead put something in their .bashrc manually, then that information > should be discoverable somehow. We shouldn=E2=80=99t need to document this at all; we should patch Conda to= do mostly the right thing. This involves limiting =E2=80=9Cconda init=E2=80= =9D to user-level changes. --=20 Ricardo
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at 42920) by debbugs.gnu.org; 20 Aug 2020 17:38:55 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Aug 20 13:38:55 2020 Received: from localhost ([127.0.0.1]:43880 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k8oWc-0004GR-PF for submit <at> debbugs.gnu.org; Thu, 20 Aug 2020 13:38:55 -0400 Received: from mail-pl1-f176.google.com ([209.85.214.176]:45593) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1k8nb0-0006j2-Kn for 42920 <at> debbugs.gnu.org; Thu, 20 Aug 2020 12:39:23 -0400 Received: by mail-pl1-f176.google.com with SMTP id bh1so1175331plb.12 for <42920 <at> debbugs.gnu.org>; Thu, 20 Aug 2020 09:39:22 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=L1Q2RCOmFFFesk3NijohkvIjX+5gM7TyWvbOqMEmNCo=; b=fZtW8AyKBJQ6t7uKR10I6DLruTJn3JoI/KpESOp6FnZ6NSBgSdJ76oU68CYDoZkoHF EExC5dTvsHSL6LdHpvmZ83bjs+uceGmhslbFqnj5+07n5Gl7r5vDDVs/pEfc12NC9FU0 r+Md2lZyon5rG8A+HnuArrwQ/QBixlmU9Ka5Y+4YYv4H8ZUzsb+x9ta/OtMhhr87X8K6 /GfY2Rg1q1blOPv7MLT0snFS9TUSnDR8Jf1/tWthtWYN2UJqCSOTQL+US2uDRB1FKFtF rerHyyP50aALqXtcYJOhf9zqDLXOW1lPjXr3u4M/e3V/8wsMRmsZyl74Zsj0Fgd5Brrm 9uHQ== X-Gm-Message-State: AOAM530Y4eQGTvBkDVZoY7FYYieIYJDEmnb5zgV/gravDOA8DMCBxXTk hrv76Kz0sp6X3l+9dpm3WsFgFntxLfoHrFZUNGusrEsSl180tg== X-Google-Smtp-Source: ABdhPJxzylV1GUCLTPUiMyW3hOeMt2lDCOAylRD+RnaRCxr7vT+qWSXNzr8fO9bvsAzCZS58gHGqlnvO7dHdC79eoyQ= X-Received: by 2002:a17:90a:fb4b:: with SMTP id iq11mr3152803pjb.127.1597941556452; Thu, 20 Aug 2020 09:39:16 -0700 (PDT) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> In-Reply-To: <87blj7x841.fsf@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Thu, 20 Aug 2020 18:39:05 +0200 Message-ID: <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="000000000000d823d105ad51c234" X-Spam-Score: 0.5 (/) X-Debbugs-Envelope-To: 42920 X-Mailman-Approved-At: Thu, 20 Aug 2020 13:38:52 -0400 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.5 (/) --000000000000d823d105ad51c234 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Ricardo, On Wed, 19 Aug 2020 at 12:07, Ricardo Wurmus <rekado@HIDDEN> wrote: > > > The conda 4.8.3 package on guix does not seem to work as expected. > > Thanks for letting me know. The upgrade took a long time and required > quite a bit of patching. > Thanks for doing this hard work! It is much appreciated, I don't think I would have started experimenting with guix without your head start. > > But activating it does not work properly: > > > > hugo@alex ~$ conda activate testenv > > > > CommandNotFoundError: Your shell has not been properly configured to us= e > > 'conda activate'. > > To initialize your shell, run > > > > $ conda init <SHELL_NAME> > > This is very unfortunate, but perhaps we can work around this. > Initially I noticed that almost none of the Conda features worked > without =E2=80=9Cconda init=E2=80=9D, so I decided to run =E2=80=9Cconda = init=E2=80=9D as part of the > build. This installs a whole bunch of shell initialization files into > the prefix directory, which =E2=80=94 I assume =E2=80=94 are meant to be = evaluated when > the shell starts. > > So I suspect that you can get around this by manually sourcing the > appropriate shell init files. Which of these need to be sourced > probably depends on your current shell. > That indeed kinda works. `conda init bash` adds this to `.bashrc` (apparently before asking for the sudo password): # >>> conda initialize >>> # !! Contents within this block are managed by 'conda init' !! __conda_setup=3D"$('/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3= /bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/cond= a.sh" ]; then . "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/cond= a.sh" else export PATH=3D"/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin:$PATH" fi fi unset __conda_setup # <<< conda initialize <<< And running this will indeed allow an environment to be activated. The `testenv3` environment contains only Python: hugo@alex ~$ which python which: no python in (/run/setuid-programs:/home/hugo/.config/guix/current/bin:/home/hugo/.guix-= profile/bin:/run/current-system/profile/bin:/run/current-system/profile/sbi= n) hugo@alex ~$ source .bashrc (base) conda activate testenv3 (testenv3) (testenv3) which python /home/hugo/.conda/envs/testenv3/bin/python (testenv3) python -bash: /home/hugo/.conda/envs/testenv3/bin/python: No such file or director= y (testenv3) readelf --all $(which python) | grep interpreter [Requesting program interpreter: /lib64/ld-linux-x86-64.so.2] So there are three problems: 1. The PATHS in .bashrc should be to ~/.guix-profile/etc/profile.d/, not to /gnu/store directly. This is trivial to fix manually. 2. The prompt is not set correctly, as in, what should happen is that the current conda environment is added to the prompt. Instead, the prompt is replaced entirely by the environment. This shouldn't be too hard to fix manually though. 3. The installed software does not have the proper interpreter set. This can probably be fixed with patchelf, but now I'm wondering whether this is the right approach, because that would be necessary for all packages installed through conda. (Or is there a way to do that automatically? Apparently just symlinking ld-linux-x86.so.2 into (from?) /lib64 also works, but that feels like a very un-guixy hack.) Sidenote, FWIW, there are also some problems with some of the scripts installed in /gnu/store: hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda -bash: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/python: bad interpreter: No such file or directory hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line 3: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-real: Permission denied /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line 3: exec: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-real: cannot execute: Permission denied It seems not necessary to actually use these scripts though. Ultimately it would be nice if all conda packages would be available in guix directly (as guix packages, removing the need for conda), but that is going to take a while. The above workarounds are probably sufficient to get something going until then. Once we settle on a good way to approach this, where should we document this? As in, if we want users to ignore the complaints from conda and instead put something in their .bashrc manually, then that information should be discoverable somehow. > FWIW, maybe it would be simpler to create a micromamba package than a > conda > > package: > > https://github.com/TheSnakePit/mamba > > Why not both? > Maybe I'll give it a shot. (micro)mamba is still a bit unstable it seems, but it might be a good fit for guix. Cheers, Hugo --000000000000d823d105ad51c234 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hi Ricardo,<br></div><br><div class=3D"gmail_quote"><= div dir=3D"ltr" class=3D"gmail_attr">On Wed, 19 Aug 2020 at 12:07, Ricardo = Wurmus <<a href=3D"mailto:rekado@HIDDEN">rekado@HIDDEN</a>>= wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px = 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br> > The conda 4.8.3 package on guix does not seem to work as expected.<br> <br> Thanks for letting me know.=C2=A0 The upgrade took a long time and required= <br> quite a bit of patching.<br></blockquote><div><br></div><div>Thanks for doi= ng this hard work! It is much appreciated, I don't think I would have s= tarted experimenting with guix without your head start.<br></div><div>=C2= =A0<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px = 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> > But activating it does not work properly:<br> ><br> > hugo@alex ~$ conda activate testenv<br> ><br> > CommandNotFoundError: Your shell has not been properly configured to u= se<br> > 'conda activate'.<br> > To initialize your shell, run<br> ><br> >=C2=A0 =C2=A0 =C2=A0$ conda init <SHELL_NAME><br> <br> This is very unfortunate, but perhaps we can work around this.<br> Initially I noticed that almost none of the Conda features worked<br> without =E2=80=9Cconda init=E2=80=9D, so I decided to run =E2=80=9Cconda in= it=E2=80=9D as part of the<br> build.=C2=A0 This installs a whole bunch of shell initialization files into= <br> the prefix directory, which =E2=80=94 I assume =E2=80=94 are meant to be ev= aluated when<br> the shell starts.<br> <br> So I suspect that you can get around this by manually sourcing the<br> appropriate shell init files.=C2=A0 Which of these need to be sourced<br> probably depends on your current shell.<br></blockquote><div><br></div><div= >That indeed kinda works. `conda init bash` adds this to `.bashrc` (apparen= tly before asking for the sudo password):</div><div><br></div><div># >&g= t;> conda initialize >>><br># !! Contents within this block are= managed by 'conda init' !!<br>__conda_setup=3D"$('/gnu/st= ore/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda' 'shell.= bash' 'hook' 2> /dev/null)"<br>if [ $? -eq 0 ]; then<br= >=C2=A0 =C2=A0 eval "$__conda_setup"<br>else<br>=C2=A0 =C2=A0 if = [ -f "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/prof= ile.d/conda.sh" ]; then<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 . "/gnu/st= ore/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.sh&quo= t;<br>=C2=A0 =C2=A0 else<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 export PATH=3D"= ;/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin:$PATH"<br= >=C2=A0 =C2=A0 fi<br>fi<br>unset __conda_setup<br># <<< conda init= ialize <<<<br></div><div><br></div><div>And running this will inde= ed allow an environment to be activated. The `testenv3` environment contain= s only Python:</div><div><br></div><div>hugo@alex ~$ which python<br>which:= no python in (/run/setuid-programs:/home/hugo/.config/guix/current/bin:/ho= me/hugo/.guix-profile/bin:/run/current-system/profile/bin:/run/current-syst= em/profile/sbin)<br>hugo@alex ~$ source .bashrc<br>(base) conda activate te= stenv3<br>(testenv3) <br>(testenv3) which python<br>/home/hugo/.conda/envs/= testenv3/bin/python<br>(testenv3) python<br>-bash: /home/hugo/.conda/envs/t= estenv3/bin/python: No such file or directory<br></div><div>(testenv3) read= elf --all $(which python) | grep interpreter<br>=C2=A0 =C2=A0 =C2=A0 [Reque= sting program interpreter: /lib64/ld-linux-x86-64.so.2]<br></div><div><br><= /div><div>So there are three problems:</div><div><br></div><div><div>1. The= PATHS in .bashrc should be to ~/.guix-profile/etc/profile.d/, not to /gnu/= store directly. This is trivial to fix manually.<br></div></div><div><br></= div><div>2. The prompt is not set correctly, as in, what should happen is t= hat the current conda environment is added to the prompt. Instead, the prom= pt is replaced entirely by the environment. This shouldn't be too hard = to fix manually though.<br></div><div><br></div><div>3. The installed softw= are does not have the proper interpreter set. This can probably be fixed wi= th patchelf, but now I'm wondering whether this is the right approach, = because that would be necessary for all packages installed through conda. (= Or is there a way to do that automatically? Apparently just symlinking ld-l= inux-x86.so.2 into (from?) /lib64 also works, but that feels like a very un= -guixy hack.)<br></div><div><br></div><div><div>Sidenote, FWIW, there are a= lso some problems with some of the scripts installed in /gnu/store:</div><d= iv><br></div>hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda= -4.8.3/condabin/conda<br>-bash: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx= -conda-4.8.3/condabin/conda: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-co= nda-4.8.3/bin/python: bad interpreter: No such file or directory<br><div>hu= go@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/acti= vate <br>/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activa= te: line 3: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.ac= tivate-real: Permission denied<br>/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518w= mx-conda-4.8.3/bin/activate: line 3: exec: /gnu/store/ihn8dbs84rmc3ai7r1vkv= h4cya518wmx-conda-4.8.3/bin/.activate-real: cannot execute: Permission deni= ed<br></div></div><div><br></div><div>It seems not necessary to actually us= e these scripts though. <br></div><div><br></div><div>Ultimately it would b= e nice if all conda packages would be available in guix directly (as guix p= ackages, removing the need for conda), but that is going to take a while. T= he above workarounds are probably sufficient to get something going until t= hen.<br></div><div><br></div><div>Once we settle on a good way to approach = this, where should we document this? As in, if we want users to ignore the = complaints from conda and instead put something in their .bashrc manually, = then that information should be discoverable somehow.</div><div><br></div><= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex"> > FWIW, maybe it would be simpler to create a micromamba package than a = conda<br> > package:<br> > <a href=3D"https://github.com/TheSnakePit/mamba" rel=3D"noreferrer" ta= rget=3D"_blank">https://github.com/TheSnakePit/mamba</a><br> <br> Why not both?<br></blockquote><div><br></div><div>Maybe I'll give it a = shot. (micro)mamba is still a bit unstable it seems, but it might be a good= fit for guix. <br></div><div><br></div><div>Cheers,</div><div>Hugo</div><d= iv><br></div></div></div> --000000000000d823d105ad51c234--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at submit) by debbugs.gnu.org; 20 Aug 2020 17:38:54 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Aug 20 13:38:54 2020 Received: from localhost ([127.0.0.1]:43878 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k8oWb-0004GO-NS for submit <at> debbugs.gnu.org; Thu, 20 Aug 2020 13:38:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:34602) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1k8naz-0006j9-51 for submit <at> debbugs.gnu.org; Thu, 20 Aug 2020 12:39:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59394) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1k8nay-0001k4-UU for bug-guix@HIDDEN; Thu, 20 Aug 2020 12:39:20 -0400 Received: from mail-pj1-f49.google.com ([209.85.216.49]:38580) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1k8naw-0003X5-FT for bug-guix@HIDDEN; Thu, 20 Aug 2020 12:39:20 -0400 Received: by mail-pj1-f49.google.com with SMTP id ep8so1220324pjb.3 for <bug-guix@HIDDEN>; Thu, 20 Aug 2020 09:39:17 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=L1Q2RCOmFFFesk3NijohkvIjX+5gM7TyWvbOqMEmNCo=; b=K0vx51W/pX4GgVyYrpReSXDwhXtWQWL52B4Lh5lFZEPoh9a/jB23l2/homMNT0ZzPJ SIYkNo17Yi3gJk82stozQdyNWfLbI4krwIG8RJzyis4PsV/qGmNSxUgQOnqTFMrkk/Wj xs2rFXghChzQDXKsMzTWaXvBvcijSHEvKdGLoJy/o6jUuxqkFMh7usYO9Ekq5SnWWNmu txl64XsgQgRf0eg5muyGTTBrC0+4UFwkcZKcuW74t1aD3h9I34+jaIp04Ld/Pg+8otye FBtuHZ4Fjf4uA1H2zzhzAAnAFiWaGFj3nIMos1S08ORAT2DZxjbm1ier6HZ24bxTqvFS 5fOA== X-Gm-Message-State: AOAM530nLA4bZQzAoqvOZfSkX1ScjMISRkd897WaqGh034vUA3z3gQHn gp5pHXSlrGbsmENd4yd3gI+uUH1TDzOLmWYStcI= X-Google-Smtp-Source: ABdhPJxzylV1GUCLTPUiMyW3hOeMt2lDCOAylRD+RnaRCxr7vT+qWSXNzr8fO9bvsAzCZS58gHGqlnvO7dHdC79eoyQ= X-Received: by 2002:a17:90a:fb4b:: with SMTP id iq11mr3152803pjb.127.1597941556452; Thu, 20 Aug 2020 09:39:16 -0700 (PDT) MIME-Version: 1.0 References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> <87blj7x841.fsf@HIDDEN> In-Reply-To: <87blj7x841.fsf@HIDDEN> From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Thu, 20 Aug 2020 18:39:05 +0200 Message-ID: <CA+Jv8O0g44LWn7_FDHNjRRq61bYYG_AMoYr3BgyHU-_tD_1UCQ@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/alternative; boundary="000000000000d823d105ad51c234" Received-SPF: pass client-ip=209.85.216.49; envelope-from=blackshift@HIDDEN; helo=mail-pj1-f49.google.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/20 12:39:17 X-ACL-Warn: Detected OS = Linux 2.2.x-3.x [generic] [fuzzy] X-Spam_score_int: 1 X-Spam_score: 0.1 X-Spam_bar: / X-Spam_report: (0.1 / 5.0 requ) BAYES_00=-1.9, FREEMAIL_FORGED_FROMDOMAIN=1, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=1, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H3=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.8 (/) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Thu, 20 Aug 2020 13:38:52 -0400 Cc: bug-guix@HIDDEN, 42920 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.8 (-) --000000000000d823d105ad51c234 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Ricardo, On Wed, 19 Aug 2020 at 12:07, Ricardo Wurmus <rekado@HIDDEN> wrote: > > > The conda 4.8.3 package on guix does not seem to work as expected. > > Thanks for letting me know. The upgrade took a long time and required > quite a bit of patching. > Thanks for doing this hard work! It is much appreciated, I don't think I would have started experimenting with guix without your head start. > > But activating it does not work properly: > > > > hugo@alex ~$ conda activate testenv > > > > CommandNotFoundError: Your shell has not been properly configured to us= e > > 'conda activate'. > > To initialize your shell, run > > > > $ conda init <SHELL_NAME> > > This is very unfortunate, but perhaps we can work around this. > Initially I noticed that almost none of the Conda features worked > without =E2=80=9Cconda init=E2=80=9D, so I decided to run =E2=80=9Cconda = init=E2=80=9D as part of the > build. This installs a whole bunch of shell initialization files into > the prefix directory, which =E2=80=94 I assume =E2=80=94 are meant to be = evaluated when > the shell starts. > > So I suspect that you can get around this by manually sourcing the > appropriate shell init files. Which of these need to be sourced > probably depends on your current shell. > That indeed kinda works. `conda init bash` adds this to `.bashrc` (apparently before asking for the sudo password): # >>> conda initialize >>> # !! Contents within this block are managed by 'conda init' !! __conda_setup=3D"$('/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3= /bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/cond= a.sh" ]; then . "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/cond= a.sh" else export PATH=3D"/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin:$PATH" fi fi unset __conda_setup # <<< conda initialize <<< And running this will indeed allow an environment to be activated. The `testenv3` environment contains only Python: hugo@alex ~$ which python which: no python in (/run/setuid-programs:/home/hugo/.config/guix/current/bin:/home/hugo/.guix-= profile/bin:/run/current-system/profile/bin:/run/current-system/profile/sbi= n) hugo@alex ~$ source .bashrc (base) conda activate testenv3 (testenv3) (testenv3) which python /home/hugo/.conda/envs/testenv3/bin/python (testenv3) python -bash: /home/hugo/.conda/envs/testenv3/bin/python: No such file or director= y (testenv3) readelf --all $(which python) | grep interpreter [Requesting program interpreter: /lib64/ld-linux-x86-64.so.2] So there are three problems: 1. The PATHS in .bashrc should be to ~/.guix-profile/etc/profile.d/, not to /gnu/store directly. This is trivial to fix manually. 2. The prompt is not set correctly, as in, what should happen is that the current conda environment is added to the prompt. Instead, the prompt is replaced entirely by the environment. This shouldn't be too hard to fix manually though. 3. The installed software does not have the proper interpreter set. This can probably be fixed with patchelf, but now I'm wondering whether this is the right approach, because that would be necessary for all packages installed through conda. (Or is there a way to do that automatically? Apparently just symlinking ld-linux-x86.so.2 into (from?) /lib64 also works, but that feels like a very un-guixy hack.) Sidenote, FWIW, there are also some problems with some of the scripts installed in /gnu/store: hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda -bash: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/python: bad interpreter: No such file or directory hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line 3: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-real: Permission denied /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate: line 3: exec: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.activate-real: cannot execute: Permission denied It seems not necessary to actually use these scripts though. Ultimately it would be nice if all conda packages would be available in guix directly (as guix packages, removing the need for conda), but that is going to take a while. The above workarounds are probably sufficient to get something going until then. Once we settle on a good way to approach this, where should we document this? As in, if we want users to ignore the complaints from conda and instead put something in their .bashrc manually, then that information should be discoverable somehow. > FWIW, maybe it would be simpler to create a micromamba package than a > conda > > package: > > https://github.com/TheSnakePit/mamba > > Why not both? > Maybe I'll give it a shot. (micro)mamba is still a bit unstable it seems, but it might be a good fit for guix. Cheers, Hugo --000000000000d823d105ad51c234 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hi Ricardo,<br></div><br><div class=3D"gmail_quote"><= div dir=3D"ltr" class=3D"gmail_attr">On Wed, 19 Aug 2020 at 12:07, Ricardo = Wurmus <<a href=3D"mailto:rekado@HIDDEN">rekado@HIDDEN</a>>= wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px = 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br> > The conda 4.8.3 package on guix does not seem to work as expected.<br> <br> Thanks for letting me know.=C2=A0 The upgrade took a long time and required= <br> quite a bit of patching.<br></blockquote><div><br></div><div>Thanks for doi= ng this hard work! It is much appreciated, I don't think I would have s= tarted experimenting with guix without your head start.<br></div><div>=C2= =A0<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px = 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> > But activating it does not work properly:<br> ><br> > hugo@alex ~$ conda activate testenv<br> ><br> > CommandNotFoundError: Your shell has not been properly configured to u= se<br> > 'conda activate'.<br> > To initialize your shell, run<br> ><br> >=C2=A0 =C2=A0 =C2=A0$ conda init <SHELL_NAME><br> <br> This is very unfortunate, but perhaps we can work around this.<br> Initially I noticed that almost none of the Conda features worked<br> without =E2=80=9Cconda init=E2=80=9D, so I decided to run =E2=80=9Cconda in= it=E2=80=9D as part of the<br> build.=C2=A0 This installs a whole bunch of shell initialization files into= <br> the prefix directory, which =E2=80=94 I assume =E2=80=94 are meant to be ev= aluated when<br> the shell starts.<br> <br> So I suspect that you can get around this by manually sourcing the<br> appropriate shell init files.=C2=A0 Which of these need to be sourced<br> probably depends on your current shell.<br></blockquote><div><br></div><div= >That indeed kinda works. `conda init bash` adds this to `.bashrc` (apparen= tly before asking for the sudo password):</div><div><br></div><div># >&g= t;> conda initialize >>><br># !! Contents within this block are= managed by 'conda init' !!<br>__conda_setup=3D"$('/gnu/st= ore/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda' 'shell.= bash' 'hook' 2> /dev/null)"<br>if [ $? -eq 0 ]; then<br= >=C2=A0 =C2=A0 eval "$__conda_setup"<br>else<br>=C2=A0 =C2=A0 if = [ -f "/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/prof= ile.d/conda.sh" ]; then<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 . "/gnu/st= ore/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.sh&quo= t;<br>=C2=A0 =C2=A0 else<br>=C2=A0 =C2=A0 =C2=A0 =C2=A0 export PATH=3D"= ;/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin:$PATH"<br= >=C2=A0 =C2=A0 fi<br>fi<br>unset __conda_setup<br># <<< conda init= ialize <<<<br></div><div><br></div><div>And running this will inde= ed allow an environment to be activated. The `testenv3` environment contain= s only Python:</div><div><br></div><div>hugo@alex ~$ which python<br>which:= no python in (/run/setuid-programs:/home/hugo/.config/guix/current/bin:/ho= me/hugo/.guix-profile/bin:/run/current-system/profile/bin:/run/current-syst= em/profile/sbin)<br>hugo@alex ~$ source .bashrc<br>(base) conda activate te= stenv3<br>(testenv3) <br>(testenv3) which python<br>/home/hugo/.conda/envs/= testenv3/bin/python<br>(testenv3) python<br>-bash: /home/hugo/.conda/envs/t= estenv3/bin/python: No such file or directory<br></div><div>(testenv3) read= elf --all $(which python) | grep interpreter<br>=C2=A0 =C2=A0 =C2=A0 [Reque= sting program interpreter: /lib64/ld-linux-x86-64.so.2]<br></div><div><br><= /div><div>So there are three problems:</div><div><br></div><div><div>1. The= PATHS in .bashrc should be to ~/.guix-profile/etc/profile.d/, not to /gnu/= store directly. This is trivial to fix manually.<br></div></div><div><br></= div><div>2. The prompt is not set correctly, as in, what should happen is t= hat the current conda environment is added to the prompt. Instead, the prom= pt is replaced entirely by the environment. This shouldn't be too hard = to fix manually though.<br></div><div><br></div><div>3. The installed softw= are does not have the proper interpreter set. This can probably be fixed wi= th patchelf, but now I'm wondering whether this is the right approach, = because that would be necessary for all packages installed through conda. (= Or is there a way to do that automatically? Apparently just symlinking ld-l= inux-x86.so.2 into (from?) /lib64 also works, but that feels like a very un= -guixy hack.)<br></div><div><br></div><div><div>Sidenote, FWIW, there are a= lso some problems with some of the scripts installed in /gnu/store:</div><d= iv><br></div>hugo@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda= -4.8.3/condabin/conda<br>-bash: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx= -conda-4.8.3/condabin/conda: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-co= nda-4.8.3/bin/python: bad interpreter: No such file or directory<br><div>hu= go@alex ~$ /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/acti= vate <br>/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activa= te: line 3: /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/.ac= tivate-real: Permission denied<br>/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518w= mx-conda-4.8.3/bin/activate: line 3: exec: /gnu/store/ihn8dbs84rmc3ai7r1vkv= h4cya518wmx-conda-4.8.3/bin/.activate-real: cannot execute: Permission deni= ed<br></div></div><div><br></div><div>It seems not necessary to actually us= e these scripts though. <br></div><div><br></div><div>Ultimately it would b= e nice if all conda packages would be available in guix directly (as guix p= ackages, removing the need for conda), but that is going to take a while. T= he above workarounds are probably sufficient to get something going until t= hen.<br></div><div><br></div><div>Once we settle on a good way to approach = this, where should we document this? As in, if we want users to ignore the = complaints from conda and instead put something in their .bashrc manually, = then that information should be discoverable somehow.</div><div><br></div><= blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l= eft:1px solid rgb(204,204,204);padding-left:1ex"> > FWIW, maybe it would be simpler to create a micromamba package than a = conda<br> > package:<br> > <a href=3D"https://github.com/TheSnakePit/mamba" rel=3D"noreferrer" ta= rget=3D"_blank">https://github.com/TheSnakePit/mamba</a><br> <br> Why not both?<br></blockquote><div><br></div><div>Maybe I'll give it a = shot. (micro)mamba is still a bit unstable it seems, but it might be a good= fit for guix. <br></div><div><br></div><div>Cheers,</div><div>Hugo</div><d= iv><br></div></div></div> --000000000000d823d105ad51c234--
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at submit) by debbugs.gnu.org; 19 Aug 2020 10:06:59 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Aug 19 06:06:59 2020 Received: from localhost ([127.0.0.1]:37930 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k8Kzi-0005Wu-QP for submit <at> debbugs.gnu.org; Wed, 19 Aug 2020 06:06:59 -0400 Received: from lists.gnu.org ([209.51.188.17]:57598) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1k8Kzg-0005Wl-UU for submit <at> debbugs.gnu.org; Wed, 19 Aug 2020 06:06:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:55524) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <rekado@HIDDEN>) id 1k8Kzg-0000iv-Iv for bug-guix@HIDDEN; Wed, 19 Aug 2020 06:06:56 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21132) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_CBC_SHA1:256) (Exim 4.90_1) (envelope-from <rekado@HIDDEN>) id 1k8Kze-0006JO-Fe for bug-guix@HIDDEN; Wed, 19 Aug 2020 06:06:56 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1597831607; cv=none; d=zohomail.com; s=zohoarc; b=llp/m6Nffty5CpLVmChjFslXD84PacENCzF7jKxmN92OU2nwChrOhvuv1dfkwxbGq2Y/CfvvvJTNh8HY6cbLKb4NHH05WW0QEw/maizyEVBssphlst6wONXZRSIGdcPheQx+erh14RRQ0Qy0aH55dVB9m4oSBHyaajAZFFTfBM8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1597831607; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Ibn9EzyfNn0KPNyd2khCGs6iQHWvRndanqkzUBlxGTs=; b=A86wkqzLqbQVLObbO+ONpEhpom1l2z8LX6VI0bbFWQ5/Mmkv2jMOvhQLOrNH2gIkfXAmjIJVCdJXjRUmrVYGCRGbfFJWbj2hx5HTmdhTEWY4H31WoggKeZViPdkEtNBF1UQS+Lbo7QdKxH9jvcLZ1rx+j5pHFWz2lfiI1aNQgDk= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1597831607; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=Ibn9EzyfNn0KPNyd2khCGs6iQHWvRndanqkzUBlxGTs=; b=gdQ4aAkEDIHGbrCdemq/ELgoeCviY7zQRVSmjw3L+ItKROaNGODd0d8LFkCJbxGL O78qxYjvBTqvDDTfIfZy4CZe/5rKmFHlRQplwmH73/tsSaM8zZGbWZ9cd0N/dz0YgHp zUEaKGnFTwtC1YLwfiz22dh3tX+f1u8WRp+ksr1c= Received: from localhost (p54ad4c52.dip0.t-ipconnect.de [84.173.76.82]) by mx.zohomail.com with SMTPS id 1597831602234994.0909613050062; Wed, 19 Aug 2020 03:06:42 -0700 (PDT) References: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> User-agent: mu4e 1.4.10; emacs 26.3 From: Ricardo Wurmus <rekado@HIDDEN> To: Hugo Buddelmeijer <hugo@HIDDEN> Subject: Re: conda 4.8.3 on guix cannot activate environments In-reply-to: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Wed, 19 Aug 2020 12:06:38 +0200 Message-ID: <87blj7x841.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Received-SPF: pass client-ip=136.143.188.51; envelope-from=rekado@HIDDEN; helo=sender4-of-o51.zoho.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/19 06:06:50 X-ACL-Warn: Detected OS = Linux 3.11 and newer [fuzzy] X-Spam_score_int: -30 X-Spam_score: -3.1 X-Spam_bar: --- X-Spam_report: (-3.1 / 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, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H2=-1, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: bug-guix@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -2.3 (--) Hi Hugo, > The conda 4.8.3 package on guix does not seem to work as expected. Thanks for letting me know. The upgrade took a long time and required quite a bit of patching. > But activating it does not work properly: > > hugo@alex ~$ conda activate testenv > > CommandNotFoundError: Your shell has not been properly configured to use > 'conda activate'. > To initialize your shell, run > > $ conda init <SHELL_NAME> This is very unfortunate, but perhaps we can work around this. Initially I noticed that almost none of the Conda features worked without =E2=80=9Cconda init=E2=80=9D, so I decided to run =E2=80=9Cconda in= it=E2=80=9D as part of the build. This installs a whole bunch of shell initialization files into the prefix directory, which =E2=80=94 I assume =E2=80=94 are meant to be ev= aluated when the shell starts. So I suspect that you can get around this by manually sourcing the appropriate shell init files. Which of these need to be sourced probably depends on your current shell. > Unfortunately, conda init does not work well, because it needs root > access: [=E2=80=A6] Yeah, it=E2=80=99s a terrible design decision on the part of the Conda developers. Luckily you won=E2=80=99t need any of that because we already installed all these files at build time. > FWIW, maybe it would be simpler to create a micromamba package than a con= da > package: > https://github.com/TheSnakePit/mamba Why not both? --=20 Ricardo
bug-guix@HIDDEN
:bug#42920
; Package guix
.
Full text available.Received: (at submit) by debbugs.gnu.org; 18 Aug 2020 19:24:32 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Aug 18 15:24:32 2020 Received: from localhost ([127.0.0.1]:37065 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1k87Di-0006dd-Eo for submit <at> debbugs.gnu.org; Tue, 18 Aug 2020 15:24:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:51802) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <blackshift@HIDDEN>) id 1k86yA-0006Ei-7S for submit <at> debbugs.gnu.org; Tue, 18 Aug 2020 15:08:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54604) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1k86yA-0008TS-0R for bug-guix@HIDDEN; Tue, 18 Aug 2020 15:08:26 -0400 Received: from mail-pl1-f180.google.com ([209.85.214.180]:32904) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from <blackshift@HIDDEN>) id 1k86y7-0003Vp-Nu for bug-guix@HIDDEN; Tue, 18 Aug 2020 15:08:25 -0400 Received: by mail-pl1-f180.google.com with SMTP id q19so9673364pll.0 for <bug-guix@HIDDEN>; Tue, 18 Aug 2020 12:08:23 -0700 (PDT) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to:cc; bh=PDjmq30sEnFkYCj+6xSa0ohES4lYo3trosGGUiP4w1I=; b=NzEh0ngSowCB2Li+g82xzsZw3/5LQZQqlJ9vZbDl2Edawl/RG8FyyXwhaFObXCQZUx ko10uAt3TFMjZJiuW17k2YqZ/fdHORATTBvzyEzh0n8CliACCoalN/uZcPWqZiKgwCRa YlMUOaeS+4l5a8Uaox4QfvF+gohEu67u/4773MlV8M/TtMR8HhFLw8XMdQ6ElEfaBSHh rsrkXUQ7vrh8UHtrgmkv4vLevP3ATVpsAVQs+PBk11qfsHJ3DuYS/iXNwIaNtlSSA3Xh g8bIeNKOA0dDBz1izoGt3VXYbMMu+EexKLFoXCZxHvIlohT/7ba3XypYpRKJVJ2Dhu1w 20pw== X-Gm-Message-State: AOAM530iTZ0aK4pvdxjOZ9hkADIjAO1duz//gESH8AlQuzC+6zY9iTvz JdKHNF9QfkV7hb+2V/YmEWjLX9jMKoe+q2CHtNG58F8TwsbyDg== X-Google-Smtp-Source: ABdhPJzt8bmARXXZzq7CsKlQhHOJifs4QGoREDcKTzw/JXM7hszN79tQKC5C+9Ak6EHCrJYHuOw8XNuMrc9mt3XHGdU= X-Received: by 2002:a17:902:523:: with SMTP id 32mr15768338plf.176.1597777701586; Tue, 18 Aug 2020 12:08:21 -0700 (PDT) MIME-Version: 1.0 From: Hugo Buddelmeijer <hugo@HIDDEN> Date: Tue, 18 Aug 2020 21:08:10 +0200 Message-ID: <CA+Jv8O20Yps0HjVws4gB6jeP7p-0Xs3dB7j9zX6b-n-n8e+w0g@HIDDEN> Subject: conda 4.8.3 on guix cannot activate environments To: bug-guix@HIDDEN Content-Type: multipart/alternative; boundary="000000000000554e5805ad2b9ccf" Received-SPF: pass client-ip=209.85.214.180; envelope-from=blackshift@HIDDEN; helo=mail-pl1-f180.google.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/18 15:08:22 X-ACL-Warn: Detected OS = Linux 2.2.x-3.x [generic] [fuzzy] X-Spam_score_int: 1 X-Spam_score: 0.1 X-Spam_bar: / X-Spam_report: (0.1 / 5.0 requ) BAYES_00=-1.9, FREEMAIL_FORGED_FROMDOMAIN=1, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=1, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H3=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.5 (/) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Tue, 18 Aug 2020 15:24:29 -0400 Cc: Ricardo Wurmus <rekado@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.8 (-) --000000000000554e5805ad2b9ccf Content-Type: text/plain; charset="UTF-8" Dear Ricardo et al., The conda 4.8.3 package on guix does not seem to work as expected. Conda info: hugo@alex ~$ which conda /home/hugo/.guix-profile/bin/conda hugo@alex ~$ realpath $(which conda) /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda hugo@alex ~$ conda -V conda 4.8.3 Creating an environment works fine: hugo@alex ~$ conda create -n testenv -y Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/hugo/.conda/envs/testenv Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate testenv # # To deactivate an active environment, use # # $ conda deactivate But activating it does not work properly: hugo@alex ~$ conda activate testenv CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run $ conda init <SHELL_NAME> Currently supported shells are: - bash - fish - tcsh - xonsh - zsh - powershell See 'conda init --help' for more information and options. IMPORTANT: You may need to close and restart your shell after running 'conda init'. Unfortunately, conda init does not work well, because it needs root access: hugo@alex ~$ conda init bash --dry-run no change /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/condabin/conda modified /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda modified /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda-env modified /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/activate modified /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/deactivate no change /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.sh no change /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/fish/conf.d/conda.fish no change /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/shell/condabin/Conda.psm1 no change /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/shell/condabin/conda-hook.ps1 no change /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/lib/python3.8/site-packages/xontrib/conda.xsh no change /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.csh modified /home/hugo/.bashrc ==> For changes to take effect, close and re-open your current shell. <== The last change of the conda package seems to be 638ef1e81d8 from August 13. This is my first week with guix, so I'm not even sure where to begin to debug this. FWIW, maybe it would be simpler to create a micromamba package than a conda package: https://github.com/TheSnakePit/mamba Cheers, Hugo --000000000000554e5805ad2b9ccf Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Dear Ricardo et al.,<br></div><div><br></div><div>The= conda 4.8.3 package on guix does not seem to work as expected.</div><div><= br></div><div>Conda info:</div><div><br></div><div>hugo@alex ~$ which conda= <br>/home/hugo/.guix-profile/bin/conda<br>hugo@alex ~$ realpath $(which con= da)<br>/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda<br= >hugo@alex ~$ conda -V<br>conda 4.8.3</div><div><br></div><div><br></div><d= iv>Creating an environment works fine:</div><div><br></div><div>hugo@alex ~= $ conda create -n testenv -y<br>Collecting package metadata (current_repoda= ta.json): done<br>Solving environment: done<br><br>## Package Plan ##<br><b= r>=C2=A0 environment location: /home/hugo/.conda/envs/testenv<br><br>Prepar= ing transaction: done<br>Verifying transaction: done<br>Executing transacti= on: done<br>#<br># To activate this environment, use<br>#<br># =C2=A0 =C2= =A0 $ conda activate testenv<br>#<br># To deactivate an active environment,= use<br>#<br># =C2=A0 =C2=A0 $ conda deactivate</div><div><br></div><div><b= r></div><div>But activating it does not work properly:<br></div><div><br></= div><div>hugo@alex ~$ conda activate testenv<br><br>CommandNotFoundError: Y= our shell has not been properly configured to use 'conda activate'.= <br>To initialize your shell, run<br><br>=C2=A0 =C2=A0 $ conda init <SHE= LL_NAME><br><br>Currently supported shells are:<br>=C2=A0 - bash<br>=C2= =A0 - fish<br>=C2=A0 - tcsh<br>=C2=A0 - xonsh<br>=C2=A0 - zsh<br>=C2=A0 - p= owershell<br><br>See 'conda init --help' for more information and o= ptions.<br><br>IMPORTANT: You may need to close and restart your shell afte= r running 'conda init'.</div><div><br></div><div><br></div><div>Unf= ortunately, conda init does not work well, because it needs root access:</d= iv><div><br></div><div>hugo@alex ~$ conda init bash --dry-run<br>no change = =C2=A0 =C2=A0 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/conda= bin/conda<br>modified =C2=A0 =C2=A0 =C2=A0/gnu/store/ihn8dbs84rmc3ai7r1vkvh= 4cya518wmx-conda-4.8.3/bin/conda<br>modified =C2=A0 =C2=A0 =C2=A0/gnu/store= /ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bin/conda-env<br>modified =C2= =A0 =C2=A0 =C2=A0/gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/bi= n/activate<br>modified =C2=A0 =C2=A0 =C2=A0/gnu/store/ihn8dbs84rmc3ai7r1vkv= h4cya518wmx-conda-4.8.3/bin/deactivate<br>no change =C2=A0 =C2=A0 /gnu/stor= e/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/etc/profile.d/conda.sh<br>no= change =C2=A0 =C2=A0 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8= .3/etc/fish/conf.d/conda.fish<br>no change =C2=A0 =C2=A0 /gnu/store/ihn8dbs= 84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/shell/condabin/Conda.psm1<br>no chang= e =C2=A0 =C2=A0 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wmx-conda-4.8.3/she= ll/condabin/conda-hook.ps1<br>no change =C2=A0 =C2=A0 /gnu/store/ihn8dbs84r= mc3ai7r1vkvh4cya518wmx-conda-4.8.3/lib/python3.8/site-packages/xontrib/cond= a.xsh<br>no change =C2=A0 =C2=A0 /gnu/store/ihn8dbs84rmc3ai7r1vkvh4cya518wm= x-conda-4.8.3/etc/profile.d/conda.csh<br>modified =C2=A0 =C2=A0 =C2=A0/home= /hugo/.bashrc<br><br>=3D=3D> For changes to take effect, close and re-op= en your current shell. <=3D=3D<br><br><br></div><div>The last change of = the conda package seems to be 638ef1e81d8 from August 13.</div><div><br></d= iv><div>This is my first week with guix, so I'm not even sure where to = begin to debug this.<br></div><div><br></div><div>FWIW, maybe it would be s= impler to create a micromamba package than a conda package:<br></div><div><= a href=3D"https://github.com/TheSnakePit/mamba">https://github.com/TheSnake= Pit/mamba</a></div><div><br></div><div>Cheers,</div><div>Hugo</div><div><br= ></div></div> --000000000000554e5805ad2b9ccf--
Hugo Buddelmeijer <hugo@HIDDEN>
:bug-guix@HIDDEN
.
Full text available.bug-guix@HIDDEN
:bug#42920
; Package guix
.
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