Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 14:04:55 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Apr 14 10:04:55 2022 Received: from localhost ([127.0.0.1]:56845 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nf05e-0006YK-WC for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:04:55 -0400 Received: from baptiste.telenet-ops.be ([195.130.132.51]:36350) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <maximedevos@HIDDEN>) id 1nf05d-0006YB-NA for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:04:54 -0400 Received: from ptr-bvsjgyhxw7psv60dyze.18120a2.ip6.access.telenet.be ([IPv6:2a02:1811:8c09:9d00:3c5f:2eff:feb0:ba5a]) by baptiste.telenet-ops.be with bizsmtp id Je4r2700D4UW6Th01e4rrL; Thu, 14 Apr 2022 16:04:52 +0200 Message-ID: <2944d00df0662c6e041e9bf075616dd8e5e37169.camel@HIDDEN> Subject: Re: bug#54787: importer Bioconductor: no tarball, only Git From: Maxime Devos <maximedevos@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN> Date: Thu, 14 Apr 2022 16:04:51 +0200 In-Reply-To: <87wnfrvqcw.fsf@HIDDEN> References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN> <87ilre5kvk.fsf@HIDDEN> <87wnfrvqcw.fsf@HIDDEN> Content-Type: multipart/signed; micalg="pgp-sha512"; protocol="application/pgp-signature"; boundary="=-XINam8b8N0XQ/IpdToQA" User-Agent: Evolution 3.38.3-1 MIME-Version: 1.0 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r22; t=1649945092; bh=2QFnw7I23PcWtmD5/x5TQxPCR3NeJc560amWKfy9RLc=; h=Subject:From:To:Cc:Date:In-Reply-To:References; b=W05NXOVA6Zu9WSnwW6wj2SvxYSJA+MlCAImSSeRVDkg4v5j5/VBANwbkjeSiedhIG v0MIxOrnfaKLDMX/DxXhmw0NltPqPwCMBjMxT4R8OP2Gke0rILM3JmTMVsVQ/CKFl/ /kbcrzWeFaGE4ZL4odrIVj/d0u3vhOMXe+wvzPmNfDC9yw9F42hZcnFcIKXMe8WhWS 6WQQ46fJHPN+kk1LDO1ApGDfvDf2Imjqdp1plvm951yA8K/h9ndll9k6bXwAOOB7WM rVNzrCseXobQlJQ0Ayf6igB1sdKk6mdWgKOOZEl4whWDNNtfLz3AlyFRkc6kKBJjgK tdCUU4c2g/bsQ== X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54787 Cc: 54787 <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 (-) --=-XINam8b8N0XQ/IpdToQA Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Ricardo Wurmus schreef op do 14-04-2022 om 13:43 [+0200]: > I wonder how the updater would need to be changed.=C2=A0 It would need to > know about the release branch and look for new commits in that branch > only. Perhaps <https://issues.guix.gnu.org/53144> would be useful? It adds a 'latest-git-updater' refresher that looks in a branch (or more generally, any reference, so in principle a tag that is repeatedly replaced would work as well) for the latest commit. There are some unaddressed comments though ... Greetings, Maxime. --=-XINam8b8N0XQ/IpdToQA Content-Type: application/pgp-signature; name="signature.asc" Content-Description: This is a digitally signed message part Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNATURE----- iI0EABYKADUWIQTB8z7iDFKP233XAR9J4+4iGRcl7gUCYlgqAxccbWF4aW1lZGV2 b3NAdGVsZW5ldC5iZQAKCRBJ4+4iGRcl7r53AP9DlogcwqzNVNiIbvZVv8rP8A6e 0/wj7D0y26tFjrQ7dAEAm1ci9dT/ccFlZksZTOMxdHQecUgPo/Tw2SUoPnXXswo= =zoB3 -----END PGP SIGNATURE----- --=-XINam8b8N0XQ/IpdToQA--
bug-guix@HIDDEN:bug#54787; Package guix.
Full text available.Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 14:00:42 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Apr 14 10:00:42 2022 Received: from localhost ([127.0.0.1]:56827 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nf01Z-0004xJ-Ug for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:00:42 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21042) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1nf01X-0004td-OY for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:00:40 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649944837; cv=none; d=zohomail.com; s=zohoarc; b=Zup6Q8GHoGhn01TtvxAbSrNOmA4lpAXi7WxI7yUyjb2z2xpwqZXsHJSRrzrZgua+9vooxaQLHPHO/ts7y5dv2JmoNHnlG7q4AFPxjhNpDrtT/Y/+OZwP3WG6hVn9uTdBZgeQjABNKJSN1DCUGx6ut1BBgI4w3uFCpA+B6w9rJjE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649944837; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=IKrnNCTW1zF6DinFrcbjog9s9CStBV/9JH9cGr90ePo=; b=Pb9MuTUM0TpKl+DQ+C+L8FugN1WIqFT/i6GlWueFJuoezHJSMNXRnjOJgaSC8Y3sXr7k1KvIb57xo35yBG4hoDPpMNiaSL/Chr/kNWUGts32BI9cD5u/WiKbD+M3ym+Y2CiajwXPBRuGT3UqrLrRWBdxeqp8496/kKJEtymQ3xs= 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=1649944837; 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=IKrnNCTW1zF6DinFrcbjog9s9CStBV/9JH9cGr90ePo=; b=FvYlxPhkRBeuImNS0WloUl9jtxla4JnGl8T/Fu6dM/0L8rceObJ1KefPUMC+gaJY UwQ1gWosBvGLjRH9ea9AVXYYmqFkOkQKw663B6KBdrUCcm6kCtE6xlTbTgyZibqdUnc MF4OVvxtOzRffWGCCIwSKQ2X43HNpfee2DPPwBvA= Received: from localhost (152-108-142-46.pool.kielnet.net [46.142.108.152]) by mx.zohomail.com with SMTPS id 1649944835027771.3960230007689; Thu, 14 Apr 2022 07:00:35 -0700 (PDT) References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN> <87ilre5kvk.fsf@HIDDEN> <87wnfrvqcw.fsf@HIDDEN> <86k0brzuph.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#54787: importer Bioconductor: no tarball, only Git Date: Thu, 14 Apr 2022 15:57:25 +0200 In-reply-to: <86k0brzuph.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: <87k0brvk73.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: 54787 Cc: 54787 <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 Thu, 14 Apr 2022 at 13:43, Ricardo Wurmus <rekado@HIDDEN> wrote: > >> We probably should *not* use RELEASE_3_14 (or whatever) as the commit, >> though, because that is a moving target. We need to resolve to the >> actual commit and use its hash. >> >> I wonder how the updater would need to be changed. It would need to >> know about the release branch and look for new commits in that branch >> only. > > To be honest, I have not checked the Bioconductor documentation about > their Git repo structure. What I see is: > > $ git clone https://git.bioconductor.org/packages/CHETAH > $ cd CHETAH > $ git branch -av > * master 5d5f5df [origin/master] Pass serialized S4 = instances thru updateObject() > remotes/origin/HEAD -> origin/master > remotes/origin/RELEASE_3_10 063de2d bump x.y.z version to even y prior = to creation of RELEASE_3_10 branch > remotes/origin/RELEASE_3_11 701ca7f bump x.y.z version to even y prior = to creation of RELEASE_3_11 branch > remotes/origin/RELEASE_3_12 cd3dd78 bump x.y.z version to even y prior = to creation of RELEASE_3_12 branch > remotes/origin/RELEASE_3_13 1eacdb8 bump x.y.z version to even y prior = to creation of RELEASE_3_13 branch > remotes/origin/RELEASE_3_14 03295c9 bump x.y.z version to even y prior = to creation of RELEASE_3_14 branch > remotes/origin/RELEASE_3_9 22b53f2 version bump > remotes/origin/master 5d5f5df Pass serialized S4 instances thru u= pdateObject() > > > Do we follow =E2=80=99master=E2=80=99? Is it a mirror of what Bioconduct= or names their > 3.14 release? We should not follow =E2=80=9Cmaster=E2=80=9D. That=E2=80=99s the developm= ent branch. We should follow the current release branch. > My guess was that RELEASE_3_14 mirrors their 3.14 release. Correct. >>> Well, I am also in favor to break the API and move %bioconductor-version >>> and %bioconductor-url to (guix build-system r). WDYT? It would >>> simplify some things (#36805 and #39885), I guess. >> >> We tried this before and we couldn=E2=80=99t do this because of a circul= ar >> reference. > > Well, I have something that works. So I do not know if this circular > reference is still there. If =E2=80=9Cmake as-derivation=E2=80=9D does not fail it is probably okay. >> That=E2=80=99s because the importer doesn=E2=80=99t let us specify a dif= ferent branch. >> We should add that, but it=E2=80=99s strictly separate from the migratio= n we=E2=80=99re >> about to embark on. > > I am not familiar with the updater (guix refresh -u). My plan is: > > 1. Add bioconductor-git-reference > 2. Adapt the bioconductor importer. > 3. Updater? The updater is closely connected to the importer. It just needs to be told how it can find new releases. > The question is: do we have to include the migration in the updater? Or > do we do the migration by custom scripts? We can do the migration manually. But if we end up with a broken updater I won=E2=80=99t be able to update Bioconductor packages in bulk; th= at would be a serious problem for future maintenance. > Note that, because we do not support shallow clones, the complete > sources will be a bit bigger; since they contain all the Bioconductor > history of all the packages. Doesn=E2=80=99t Guile-Git support shallow clones? In any case, this should= not be an obstacle for us. Ensuring long-term reproducibility is more important than space savings. --=20 Ricardo
bug-guix@HIDDEN:bug#54787; Package guix.
Full text available.Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 13:09:54 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Apr 14 09:09:54 2022 Received: from localhost ([127.0.0.1]:55587 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nezEQ-0002bC-D1 for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 09:09:54 -0400 Received: from mail-wr1-f45.google.com ([209.85.221.45]:33289) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1nezEO-0002aw-Td for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 09:09:53 -0400 Received: by mail-wr1-f45.google.com with SMTP id c7so6893446wrd.0 for <54787 <at> debbugs.gnu.org>; Thu, 14 Apr 2022 06:09:52 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:in-reply-to:references:date:message-id :mime-version:content-transfer-encoding; bh=RjMrVGNhwTkDMIH9KP/SO4HYW5H7AY8ymh+rCZ4hyzs=; b=RSZ5fAAajwv1qzu1VpAaCEdyvgP/tUS0nw74YyCSd4r+xEwp6CaJiPCAZ51Se7KHNE XjjXXngvhOuimWEyFJKtEBSLW7dOohBM2xK8dPw+RK+mzkxaLEwRuV0Ro6WSrf/K0ido P3dvhdCH/b2uhhohd5mFBV7gwc601TtqdWbxOS6CUpG5RikQmXDTDv7+8Brf2m8f5SW5 HYnKzDaITunn7BC1u1q9P/k2lzuEO7jdBbQHi57uEugS5cg8ZhEazI/Sn0oBsxOcdutt 6tA8lDBFUK5CtwGbd35KQHqjM/B7I5kqfnlO8WcEUEzO3o/TdmrRUYji6Tpbosp5BPeN pUPw== 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:in-reply-to:references:date :message-id:mime-version:content-transfer-encoding; bh=RjMrVGNhwTkDMIH9KP/SO4HYW5H7AY8ymh+rCZ4hyzs=; b=gY6O897Xqj3lLpTO/V1GbmjNrdkqFgW9WJD3qPz9ya2aPK1aD5Jz9s2BxtGkc0R4vu jXkUctOHaZg9hGLALvuzZ3dpLc/ZkCU1KwemYd9fqGLEq6SydDAxEIqEQxgYnNrCPciS P71hN8fd6kPnWTcX25ByO2zajsWTnbyVG9W4kKy0J5TomTVTeBpUwMkNdnrzJtXiEBy4 GEaDkzKbiElE+edPYQBOF2seeuUo90rumwmwTJ4Oixh2UHr4CinE7It3P/G+E3Q3wjGQ VG7E5CmH3GVKFctzxqGeeTwzJjRyotbaG48/ziClZz1Kv00BOKfG+hrVFiIqZbFyRSgc qrxA== X-Gm-Message-State: AOAM5337RRwGB4rShzAM6ROT0CzLWUZ0NIhGU/BTMvK4QMQuzkNmupls rYM2k/8j+kUXmiIn1TfM0dWcpf0QY1k= X-Google-Smtp-Source: ABdhPJwq5G7ymNd9fUilqvlDrdGqooIo9kK546Ro20miymuxx0qgo4Nn5FUiVM6sGrgWb3MVKEHC4A== X-Received: by 2002:a5d:53cb:0:b0:207:ab75:3ce7 with SMTP id a11-20020a5d53cb000000b00207ab753ce7mr2121740wrw.171.1649941786981; Thu, 14 Apr 2022 06:09:46 -0700 (PDT) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id s7-20020a5d6a87000000b00207aad420c4sm1730396wru.101.2022.04.14.06.09.45 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 14 Apr 2022 06:09:46 -0700 (PDT) From: zimoun <zimon.toutoune@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#54787: importer Bioconductor: no tarball, only Git In-Reply-To: <87wnfrvqcw.fsf@HIDDEN> References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN> <87ilre5kvk.fsf@HIDDEN> <87wnfrvqcw.fsf@HIDDEN> Date: Thu, 14 Apr 2022 14:59:54 +0200 Message-ID: <86k0brzuph.fsf@HIDDEN> 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: 54787 Cc: 54787 <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 Thu, 14 Apr 2022 at 13:43, Ricardo Wurmus <rekado@HIDDEN> wrote: > We probably should *not* use RELEASE_3_14 (or whatever) as the commit, > though, because that is a moving target. We need to resolve to the > actual commit and use its hash. > > I wonder how the updater would need to be changed. It would need to > know about the release branch and look for new commits in that branch > only. To be honest, I have not checked the Bioconductor documentation about their Git repo structure. What I see is: --8<---------------cut here---------------start------------->8--- $ git clone https://git.bioconductor.org/packages/CHETAH $ cd CHETAH $ git branch -av * master 5d5f5df [origin/master] Pass serialized S4 in= stances thru updateObject() remotes/origin/HEAD -> origin/master remotes/origin/RELEASE_3_10 063de2d bump x.y.z version to even y prior to= creation of RELEASE_3_10 branch remotes/origin/RELEASE_3_11 701ca7f bump x.y.z version to even y prior to= creation of RELEASE_3_11 branch remotes/origin/RELEASE_3_12 cd3dd78 bump x.y.z version to even y prior to= creation of RELEASE_3_12 branch remotes/origin/RELEASE_3_13 1eacdb8 bump x.y.z version to even y prior to= creation of RELEASE_3_13 branch remotes/origin/RELEASE_3_14 03295c9 bump x.y.z version to even y prior to= creation of RELEASE_3_14 branch remotes/origin/RELEASE_3_9 22b53f2 version bump remotes/origin/master 5d5f5df Pass serialized S4 instances thru upd= ateObject() --8<---------------cut here---------------end--------------->8--- Do we follow =E2=80=99master=E2=80=99? Is it a mirror of what Bioconductor= names their 3.14 release? My guess was that RELEASE_3_14 mirrors their 3.14 release. >> Well, I am also in favor to break the API and move %bioconductor-version >> and %bioconductor-url to (guix build-system r). WDYT? It would >> simplify some things (#36805 and #39885), I guess. > > We tried this before and we couldn=E2=80=99t do this because of a circular > reference. Well, I have something that works. So I do not know if this circular reference is still there. > That=E2=80=99s because the importer doesn=E2=80=99t let us specify a diff= erent branch. > We should add that, but it=E2=80=99s strictly separate from the migration= we=E2=80=99re > about to embark on. I am not familiar with the updater (guix refresh -u). My plan is: 1. Add bioconductor-git-reference 2. Adapt the bioconductor importer. 3. Updater? The question is: do we have to include the migration in the updater? Or do we do the migration by custom scripts? Note that, because we do not support shallow clones, the complete sources will be a bit bigger; since they contain all the Bioconductor history of all the packages. Cheers, simon
bug-guix@HIDDEN:bug#54787; Package guix.
Full text available.Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 11:47:35 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Apr 14 07:47:35 2022 Received: from localhost ([127.0.0.1]:55500 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nexwk-0000Tn-Vt for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 07:47:35 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21080) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1nexwi-0000TU-FL for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 07:47:33 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649936850; cv=none; d=zohomail.com; s=zohoarc; b=kp/M6A6OQ5ZAPnhyn7G0LE8Urbc5oPojfQW8KwhrQB56fYTD2b+1dlY3nv8q9wld8RLiPUo2EmkKLIBQN/9b9ta1bS+eT5F4JSNF2bSjdxsqPOenR6b6WRhJz9pKcWShb41qMAPtdQAkdTeKm3weo1EzwyjIyJDTCVhMOIyY56Y= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649936850; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=+rAXGJpxct5Ij19dKkv7N/6onhyaUnz5pjzo8BVMwZw=; b=Vkh1Mw+oGVz/4pKFxslAO7h+T46tl/NppKb0zJGvyhCGVYPOa3igjFEcOlOlFX2kvQ50s03gkxqHJChevWbNHH6lBi4/8P98ENpNGpbBj7YIXJQ5AMotDxL8JrzrF74f7UeE2l9k8ZcXHLCzXYGna4W60SQVTOH40+3NX4wmGEo= 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=1649936850; 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=+rAXGJpxct5Ij19dKkv7N/6onhyaUnz5pjzo8BVMwZw=; b=dvL77awij6snInHDr0go9DUfd3Bvr2JytcRqltId0VYRA6Z+Sk7pI+Q5zwwBDx/z SSzM7hCTTMD3E7VwzOYMwXxH6SPo8xnfvKf9WOhHSMei2LmUD3DgAxXLS4JdoExNxUD pplElK5XypRsd2p4oPCxbwD+jMbwNiSrMKv+zcfA= Received: from localhost (152-108-142-46.pool.kielnet.net [46.142.108.152]) by mx.zohomail.com with SMTPS id 1649936849792691.6268642098051; Thu, 14 Apr 2022 04:47:29 -0700 (PDT) References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN> <87ilre5kvk.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#54787: importer Bioconductor: no tarball, only Git Date: Thu, 14 Apr 2022 13:43:36 +0200 In-reply-to: <87ilre5kvk.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: <87wnfrvqcw.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: 54787 Cc: 54787 <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: > First, note that annotations do not have Git repo; at least not always, > e.g., > > <https://bioconductor.org/packages/release/data/annotation/html/GenomeInf= oDbData.html> That=E2=80=99s fine. We just ignore annotation and experiment packages, an= d use git only for regular packages. > Second, if we go for something like: > > (define* (bioconductor-git-reference name #:optional > (release %bioconductor-version)) > "Return a <git-reference> for the R package archive on Bioconductor for= the > RELEASE corresponding to NAME." > (git-reference > (url (string-append %bioconductor-git-url name)) > (commit (string-append "RELEASE_" (string-replace-substring > %bioconductor-version "." "_"))))) > > > then, it raises the question: import/cran.scm or build-system/r.scm ? > i.e., do we put a module dependency against (guix git-download) for the > r-build-system or not? > > TeXLive already has a dependency to svn-download, so why not. Yes, I don=E2=80=99t think that=E2=80=99s a problem. We probably should *not* use RELEASE_3_14 (or whatever) as the commit, though, because that is a moving target. We need to resolve to the actual commit and use its hash. I wonder how the updater would need to be changed. It would need to know about the release branch and look for new commits in that branch only. > Well, I am also in favor to break the API and move %bioconductor-version > and %bioconductor-url to (guix build-system r). WDYT? It would > simplify some things (#36805 and #39885), I guess. We tried this before and we couldn=E2=80=99t do this because of a circular reference. > Back to CHETAH, note that > > guix import cran -a git htpps://git.bioconductor.org/CHETAH > > works but it points to master instead of RELEASE_3_14. Well, I am not > very familiar with the Bioconductor workflow for their release. That=E2=80=99s because the importer doesn=E2=80=99t let us specify a differ= ent branch. We should add that, but it=E2=80=99s strictly separate from the migration w= e=E2=80=99re about to embark on. > Last, using this in gnu/packages/bioconductor.scm, > > (define-public r-chetah > (package > (name "r-chetah") > (version "1.11.2") > (source > (origin > (method git-fetch) > (uri (bioconductor-git-reference "CHETAH")) > (file-name (git-file-name name version)) > (sha256 > (base32 "021v5831zqdy4pirfsb35kbnz8kmz4lxqc4cwi55qgd6r081xlgh")))) > (properties `((upstream-name . "CHETAH"))) > (build-system r-build-system) > (propagated-inputs > (list r-biodist > r-corrplot > r-cowplot > r-dendextend > r-ggplot2 > r-gplots > r-pheatmap > r-plotly > r-reshape2 > r-s4vectors > r-shiny > r-singlecellexperiment > r-summarizedexperiment)) > (native-inputs (list r-knitr)) > (home-page "https://git.bioconductor.org/packages/CHETAH") > (synopsis "Fast and accurate scRNA-seq cell type identification") > (description > "CHETAH (CHaracterization of cEll Types Aided by Hierarchical classi= fication) is > an accurate, selective and fast scRNA-seq classifier. Classification is = guided > by a reference dataset, preferentially also a scRNA-seq dataset. By > hierarchical clustering of the reference data, CHETAH creates a classific= ation > tree that enables a step-wise, top-to-bottom classification. Using a nov= el > stopping rule, CHETAH classifies the input cells to the cell types of the > references and to \"intermediate types\": more general classifications th= at ended > in an intermediate node of the tree.") > (license #f))) > > it just builds with, > > ./pre-inst-env guix build r-chetah > > > > WDYT? Neat :) --=20 Ricardo
bug-guix@HIDDEN:bug#54787; Package guix.
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From: zimoun <zimon.toutoune@HIDDEN>
To: Ricardo Wurmus <rekado@HIDDEN>
Subject: Re: bug#54787: importer Bioconductor: no tarball, only Git
References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN>
Date: Tue, 12 Apr 2022 18:25:51 +0200
In-Reply-To: <874k2zzj9p.fsf@HIDDEN> (Ricardo Wurmus's message of "Mon,
11 Apr 2022 18:15:39 +0200")
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Hi Ricardo,
On lun., 11 avril 2022 at 18:15, Ricardo Wurmus <rekado@HIDDEN> wrote:
> zimoun <zimon.toutoune@HIDDEN> writes:
>
>> $ guix import cran -a bioconductor CHETAH
>> guix import: warning: failed to retrieve package information from
>> https://cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Fou=
nd)
>> guix import: error: failed to download description for package 'CHETAH'
>>
>> The reason is because there is no source package. Only the Git source
>> repo.
>
> We should finally switch to fetching the sources from Git. I wonder why
> we haven=E2=80=99t done this earlier.
Because, maybe, we have just finished the janitor work cleaning the
files cran.scm, bioconductor.scm and bioinformatics.scm. :-)
> I guess we should do this gradually to avoid mass updates, so perhaps we
> should introduce bioconductor-git-reference and switch over packages one
> by one.
First, note that annotations do not have Git repo; at least not always,
e.g.,
<https://bioconductor.org/packages/release/data/annotation/html/GenomeInfoD=
bData.html>
Second, if we go for something like:
--8<---------------cut here---------------start------------->8---
(define* (bioconductor-git-reference name #:optional
(release %bioconductor-version))
"Return a <git-reference> for the R package archive on Bioconductor for t=
he
RELEASE corresponding to NAME."
(git-reference
(url (string-append %bioconductor-git-url name))
(commit (string-append "RELEASE_" (string-replace-substring
%bioconductor-version "." "_")))))
--8<---------------cut here---------------end--------------->8---
then, it raises the question: import/cran.scm or build-system/r.scm ?
i.e., do we put a module dependency against (guix git-download) for the
r-build-system or not?
TeXLive already has a dependency to svn-download, so why not.
Well, I am also in favor to break the API and move %bioconductor-version
and %bioconductor-url to (guix build-system r). WDYT? It would
simplify some things (#36805 and #39885), I guess.
Third, the adjustments of the importer require a large cup of coffee.
Back to CHETAH, note that
guix import cran -a git htpps://git.bioconductor.org/CHETAH
works but it points to master instead of RELEASE_3_14. Well, I am not
very familiar with the Bioconductor workflow for their release.
Last, using this in gnu/packages/bioconductor.scm,
--8<---------------cut here---------------start------------->8---
(define-public r-chetah
(package
(name "r-chetah")
(version "1.11.2")
(source
(origin
(method git-fetch)
(uri (bioconductor-git-reference "CHETAH"))
(file-name (git-file-name name version))
(sha256
(base32 "021v5831zqdy4pirfsb35kbnz8kmz4lxqc4cwi55qgd6r081xlgh"))))
(properties `((upstream-name . "CHETAH")))
(build-system r-build-system)
(propagated-inputs
(list r-biodist
r-corrplot
r-cowplot
r-dendextend
r-ggplot2
r-gplots
r-pheatmap
r-plotly
r-reshape2
r-s4vectors
r-shiny
r-singlecellexperiment
r-summarizedexperiment))
(native-inputs (list r-knitr))
(home-page "https://git.bioconductor.org/packages/CHETAH")
(synopsis "Fast and accurate scRNA-seq cell type identification")
(description
"CHETAH (CHaracterization of cEll Types Aided by Hierarchical classifi=
cation) is
an accurate, selective and fast scRNA-seq classifier. Classification is gu=
ided
by a reference dataset, preferentially also a scRNA-seq dataset. By
hierarchical clustering of the reference data, CHETAH creates a classificat=
ion
tree that enables a step-wise, top-to-bottom classification. Using a novel
stopping rule, CHETAH classifies the input cells to the cell types of the
references and to \"intermediate types\": more general classifications that=
ended
in an intermediate node of the tree.")
(license #f)))
--8<---------------cut here---------------end--------------->8---
it just builds with,
./pre-inst-env guix build r-chetah
WDYT?
Cheers,
simon
bug-guix@HIDDEN:bug#54787; Package guix.
Full text available.Received: (at 54787) by debbugs.gnu.org; 11 Apr 2022 16:18:03 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Apr 11 12:18:03 2022 Received: from localhost ([127.0.0.1]:45429 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1ndwjr-0003h5-Ev for submit <at> debbugs.gnu.org; Mon, 11 Apr 2022 12:18:03 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21097) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1ndwjp-0003gb-Bb; Mon, 11 Apr 2022 12:18:01 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649693878; cv=none; d=zohomail.com; s=zohoarc; b=W6Z1cl3LZmeVLJW1UE4iU2z43oJAWuEko1oKM9ncTVJ/XOFkbSs7XKmtzqTCxFNMEcaPz4TEq6gm+GZNqM4fgJS0+KgZf1GT9vYVyMtk7+HdigaExg0K5fT9wDA9kG5G8QZtwaYnKc1VmlXUTy+It09cWKrmqLuduJnGCBdjp20= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649693878; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=xR0naLFgCGIYkHo6MXQyQ54Z/eXmZ1yYyO0I5vPDUp4=; b=NyrBRZCoVKv8cqtdTdyyvlMSuFuOYFhn5QYetDAq+5RhPXB7j4LzGJAumVnj8IpldFrMDW9xBLVltEFrlowc6gPNAItxmV1KksSUe70+vjUnyVcNA2V8DfMN/Aah+kGAVRcDdRmb3OnS7TLRjInrlGsxLKVpG6TLDO/40Vg+x64= 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=1649693878; 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=xR0naLFgCGIYkHo6MXQyQ54Z/eXmZ1yYyO0I5vPDUp4=; b=GoRL0n/d1E92B42v/NYEDxSHqW+cWqwoe/GFNxucJqaSMDcPjyi+SYFczaI4Qh0t YD4VXQg/l8E76aD64V2lJwixTzvKaE9rLrdUG40BMEX8YWRdfBUZn4RSY5JoYo82655 xilwDvuGvm6x+VJ/bnctrQzhDQ8VwRokXZjs+MLw= Received: from localhost (i5E862D75.versanet.de [94.134.45.117]) by mx.zohomail.com with SMTPS id 1649693877699188.37067792420635; Mon, 11 Apr 2022 09:17:57 -0700 (PDT) References: <868rsf23th.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#54787: importer Bioconductor: no tarball, only Git Date: Mon, 11 Apr 2022 18:15:39 +0200 In-reply-to: <868rsf23th.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: <874k2zzj9p.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: 54787 Cc: debbugs-submit <at> debbugs.gnu.org, 54787 <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: > $ guix import cran -a bioconductor CHETAH > guix import: warning: failed to retrieve package information from https:/= /cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Found) > guix import: error: failed to download description for package 'CHETAH' > > The reason is because there is no source package. Only the Git source > repo. We should finally switch to fetching the sources from Git. I wonder why we haven=E2=80=99t done this earlier. I guess we should do this gradually to avoid mass updates, so perhaps we should introduce bioconductor-git-reference and switch over packages one by one. What do you think? --=20 Ricardo
bug-guix@HIDDEN:bug#54787; Package guix.
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Fri, 08 Apr 2022 04:51:51 -0700 (PDT) Received: from lili ([88.126.110.68]) by smtp.gmail.com with ESMTPSA id o9-20020a056000010900b00206186ac25esm10942822wrx.12.2022.04.08.04.51.51 for <bug-guix@HIDDEN> (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 04:51:51 -0700 (PDT) From: zimoun <zimon.toutoune@HIDDEN> To: Bug Guix <bug-guix@HIDDEN> Subject: importer Bioconductor: no tarball, only Git X-Debbugs-CC: Ricardo Wurmus <rekado@HIDDEN> Date: Fri, 08 Apr 2022 13:48:58 +0200 Message-ID: <868rsf23th.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=2a00:1450:4864:20::42d; envelope-from=zimon.toutoune@HIDDEN; helo=mail-wr1-x42d.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit 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, Consider the package CHETAH, included in Bioconductor release 3.14; <https://bioconductor.org/packages/release/bioc/html/CHETAH.html> but then, --8<---------------cut here---------------start------------->8--- $ guix import cran -a bioconductor CHETAH guix import: warning: failed to retrieve package information from https://cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Found) guix import: error: failed to download description for package 'CHETAH' --8<---------------cut here---------------end--------------->8--- The reason is because there is no source package. Only the Git source repo. Cheers, simon
zimoun <zimon.toutoune@HIDDEN>:rekado@HIDDEN, bug-guix@HIDDEN.
Full text available.rekado@HIDDEN, bug-guix@HIDDEN:bug#54787; Package guix.
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