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Thu, 20 Aug 2020 23:53:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:33140) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1k8y6w-0007B1-5u for bug-guix@gnu.org; Thu, 20 Aug 2020 23:53:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1k8y6w-0003kQ-5A for bug-guix@gnu.org; Thu, 20 Aug 2020 23:53:02 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#42920: conda 4.8.3 on guix cannot activate environments Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Fri, 21 Aug 2020 03:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 42920 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Hugo Buddelmeijer X-Debbugs-Original-Cc: bug-guix@gnu.org, 42920@debbugs.gnu.org Received: via spool by 42920-submit@debbugs.gnu.org id=B42920.159798194614353 (code B ref 42920); Fri, 21 Aug 2020 03:53:02 +0000 Received: (at 42920) by debbugs.gnu.org; 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mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1597981926; s=zoho; d=elephly.net; i=rekado@elephly.net; 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: <87blj7x841.fsf@elephly.net> User-agent: mu4e 1.4.10; emacs 26.3 From: Ricardo Wurmus In-reply-to: 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@elephly.net> 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: 42920@debbugs.gnu.org Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=elephly.net header.s=zoho header.b=IFUve9Do; dmarc=none; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Spam-Score: 1.99 X-TUID: kEGjrx1JRQWF Hugo Buddelmeijer 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