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[194.254.61.47]) by smtp.gmail.com with ESMTPSA id a3-20020adff7c3000000b00228db6b9406sm1237736wrq.45.2022.09.09.10.30.59 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 09 Sep 2022 10:31:00 -0700 (PDT) From: zimoun In-Reply-To: <878rnwuemq.fsf@elephly.net> References: <87lesqmmrr.fsf@gmail.com> <87bktmtmol.fsf@elephly.net> <878rnwuemq.fsf@elephly.net> Date: Fri, 09 Sep 2022 19:23:12 +0200 Message-ID: <865yhwpim7.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1662744772; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=30UyClpR35f238PPvnrXeSqi8iXd3D64lce5xlpYj+Y=; b=SuKSbj53X2tnOOmYGIQ9ZBS0UiytRaXMhpzpUAZ0jS2lnjYq3mszOlQldf8S0QwNYnkqY/ iRMQeVK1xfxDyCH3yeb2uFtbZiqq0MmiIOsArcsxnNxTHx8L+W0b2rEES1CGxhKacrWFis gdUn9pCL7OqnKkSsB43AvywdxO/5VAN9UOHZSd+05+NgeDyTZd6nxPjWt7H6GaMWBqbzMq lMcLsXYiFENEv/QY8AhqgxuZGppHYL9MxUc0Stt3qXIuq9Arri06dNvTWLaTrHKfEUqIDr 7i1EYhBmgOkvm6AaTufE417mVzsIhCqBckPx2TdpVwGjbUon4OAOg5KDqa78Zw== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1662744772; a=rsa-sha256; cv=none; b=iJILHmj7ECkbFqSlPFz2rc5DKi1Q72xDNKzVqF3sgfePhpTh2j7GAr7oV4HvZt5Qg18W89 OGoYUQNpYFTWiwir9x2UHj3A+OB36JefFmZjQN4l1YAly17+p4hvCsevrZpW5SlMvk28Da ND+k2eGtulAuEx6ZG0udXQQTflE6Et9rKeKU0CYPUQVNCSKIkbNfaWykICUEteOfG122db MtCLt55RWCGSFztywvKfWcoTATufEkgmHHofWrSpDDw1QZMoh0LhyUQsJemjUU4BxG5oZt o3dyZS0KZg5sSuBwxUv8JHq7juUGBzZ8HtyESpCtjinooh843zoBgnwWfHBmXQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b="I05xII/4"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.90 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b="I05xII/4"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 2074D3A3E8 X-Spam-Score: 6.90 X-Migadu-Scanner: scn0.migadu.com X-TUID: +dCNzNuGvC+S Hi Ricardo, I am late. This message landed when I was traveling for holidays. :-) On Wed, 10 Aug 2022 at 20:25, Ricardo Wurmus wrote: > - we cannot use the updater to go from =E2=80=9Curl-fetch=E2=80=9D to =E2= =80=9Cgit-fetch=E2=80=9D. > That=E2=80=99s because =E2=80=9Cpackage-update=E2=80=9D in (guix upstre= am) decides whether to > use package-update/url-fetch or package-update/git-fetch based on the > *current* package value=E2=80=99s origin fetch procedure. For the swit= ch we > can hack around this (adding an exception for bioconductor packages), > but there is no pretty way to do this in a generic fashion that could > be committed. It appears to me acceptable to have an exception. Or even to do it just once as a big replacement of Bioconductor packages. > - the repositories at https://git.bioconductor.org/package/NAME do not > tag package versions. The only method of organization is branches > that are named after *Bioconductor releases* (not package releases), > e.g. RELEASE_3_15. We can only determine the package version by > reading its DESCRIPTION file or by looking up the version index for > all Bioconductor packages (we do that already). This means that there > could be different commits for the same package version in the same > release branch =E2=80=94 so we have to include the commit hash and a re= vision > counter in the version string. This is the most annoying part. Indeed, when I check out some Bioconductor Git repositories, I am always confused by their Git structure. >From my understanding, the tarball you fetch from bioconductor.org has the same content than the commit tagged =E2=80=9CBioconductor release=E2=80= =9D (RELEASE_X_Y). The content of the upstream release can mismatch the content of the Bioconductor tarball release. I do not know how it would be complicated or inaccurate to consider the package version from the Bioconductor index and assign this version to the commit tagged RELEASE_X_Y. This commit would appear in the Guix package definition though. Or maybe we transparently could RELEASE_X_Y to determine this commit. > - the updater doesn=E2=80=99t work on version expressions like (git-versi= on > "1.12" revision commit). It expects to be able to replace literal > strings. Because of that my changes let the importer generate a > string literal such as "1.12-0.cafebab" without a let-bound commit > string. Maxime pointed patch#53144 [1] but I have not looked at it yet. 1: > - =E2=80=9Cexperiment=E2=80=9D or =E2=80=9Cdata=E2=80=9D packages are not= kept in Git. They only exist > as volatile tarballs that will be overwritten. Thankfully, they don=E2= =80=99t > change all that often, so they have a good chance of making it into > our archives. That=E2=80=99s an interesting question for Disarchive and Software Heritage. Cheers, simon