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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 <zimon.toutoune@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine In-Reply-To: <878rnwuemq.fsf@HIDDEN> References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> Date: Fri, 09 Sep 2022 19:23:12 +0200 Message-ID: <865yhwpim7.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: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@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: -1.0 (-) Hi Ricardo, I am late. This message landed when I was traveling for holidays. :-) On Wed, 10 Aug 2022 at 20:25, Ricardo Wurmus <rekado@HIDDEN> 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: <https://issues.guix.gnu.org/53144#13> > - =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
bug-guix@HIDDEN:bug#39885; Package guix.
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rv:91.0) Gecko/20100101 Thunderbird/91.12.0 Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Content-Language: en-US From: Maxime Devos <maximedevos@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN> References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> In-Reply-To: <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="------------5NR32MArIFNI7RA2FDeUYReA" DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r22; t=1660160917; bh=MHI2K69UpMZnN+Lo+o4vxlI6vPFS6pi1rbsta96jadg=; h=Date:Subject:From:To:Cc:References:In-Reply-To; b=cRjEZpSFnrIZ7ahluPCxvh8lWcmexhaowX7Pl73l2sgEuiFy5LjIonog5qCSkkQxJ yRKZ4x0AXS3T7wJKaQtVHwUSOQfD0C2JQIcUu4Ke0mXDrffrppjg3811HdZ0eyhNTn xDW+2bSVYUWn/q7RxYgkrcbl8y3jius8YOb1g9J1b/KnmErxUJaB3jNQNQbUfDTyE7 e5DcFjh+VUbU+7ZVaPQCE6w0jisQr5/T94+mMzf6XB7Oflia2W6G0JapIU3F97k+pt Du626Wx6syh22DbOe4k0Ru8gXgXhjIRNr+/GyiJAFLRGrQnMMB5YZMsVti/PWnDC6+ HCAXZbjUwQoSQ== X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@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: -1.7 (-) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --------------5NR32MArIFNI7RA2FDeUYReA Content-Type: multipart/mixed; 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bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 10 Aug 2022 19:44:54 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Aug 10 15:44:54 2022 Received: from localhost ([127.0.0.1]:50813 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oLrdN-0005YX-Tv for submit <at> debbugs.gnu.org; Wed, 10 Aug 2022 15:44:54 -0400 Received: from xavier.telenet-ops.be ([195.130.132.52]:37760) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <maximedevos@HIDDEN>) id 1oLrdK-0005YM-10 for 39885 <at> debbugs.gnu.org; Wed, 10 Aug 2022 15:44:52 -0400 Received: from [IPV6:2a02:1811:8c09:9d00:5dba:d409:33f7:a16] ([IPv6:2a02:1811:8c09:9d00:5dba:d409:33f7:a16]) by xavier.telenet-ops.be with bizsmtp id 5vkn2800120ykKC01vknjF; Wed, 10 Aug 2022 21:44:48 +0200 Message-ID: <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> Date: Wed, 10 Aug 2022 21:44:46 +0200 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.12.0 Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Content-Language: en-US To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN> References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> From: Maxime Devos <maximedevos@HIDDEN> In-Reply-To: <878rnwuemq.fsf@HIDDEN> Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="------------kZthixqD0lRwLYSdlfte8yIx" DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r22; t=1660160688; bh=vklUgoy0gA5SxO9KNthNg0AF2SwknnpX1WSSOz/VgZs=; h=Date:Subject:To:Cc:References:From:In-Reply-To; b=jWsyYjZzytptGQsA9UUtc9fqFqOxMr5vdriIDXvMwMbyfSIdVLCpzh32vg6TDWIqj ax4uLOfXrksuDRWQcJEv2FBJirpXEmgYCi88wMGW2z+BC8GaFDUiekDt3JxLtu2GUj WNT2nFUyGC4vhE2SGE7RYI2xYajQw5nHc7xvWQLasQn9FYAJX28XOgO62XFmpbViVu DJmNfVebJkw+O3+eWdqH/kdlcrYNdDnwvsMrE5T46zMKwTBx/lGp1GyrJjWR/40pWy Q5GBgtmpAyN/TArl76c9RONPP8XuU26dtWtMyBCi7xP7yevBtm8Ah+87Ugge2ctsN3 WHZm0KzWCgn6g== X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@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: -1.7 (-) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --------------kZthixqD0lRwLYSdlfte8yIx Content-Type: multipart/mixed; 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bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 10 Aug 2022 18:39:53 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Aug 10 14:39:53 2022 Received: from localhost ([127.0.0.1]:50758 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oLqcS-0003vd-Kr for submit <at> debbugs.gnu.org; Wed, 10 Aug 2022 14:39:52 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21186) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1oLqcN-0003vQ-K4 for 39885 <at> debbugs.gnu.org; Wed, 10 Aug 2022 14:39:51 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1660156785; cv=none; d=zohomail.com; s=zohoarc; b=oI1wx+LoiUZ66DqvhGL2gR7QrUtwZDxCHp2+bmVbD8xKmkjNU3ewmG6TVFqaLSaZyOXSVPvEsQJnuEZLVcZa+mLc9Mp+S+9l2+YIxdbEqa6ePZtZx5AVkmNIKwaGY1+QrQYqdEcjvtRWxKQ7yFzdXhq0GyBLLJCP3DL+AdDYuZk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1660156785; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=TeXmwSVxSxS260Wh7R3Zw5zrphz8e645fb7uLQEv5cQ=; b=P3NVT84apMP/W0OqPCDPmXR5w70V3xyEKXwF41o0WI5mSwVvkY5M4ljgdL6niiEND7zRuA2fsUbBqxB9vx5SWG1FhxuM9/H9jDDT3XJdmmn81exaEMAIA23tD90vmvQVX11O6yLWiORSa8C9WoBhgONcuUcocsOD7h41nk+AYDw= 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=1660156785; 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=TeXmwSVxSxS260Wh7R3Zw5zrphz8e645fb7uLQEv5cQ=; b=H/7bGZSneLGmrCs/7YoQLZqBbwOnKEtUULLVmcXphRcAtynR0MgILbKlx9bhjeB8 HLLFWcb6szztx33LqYih8XCESNZ9SY0MkQhA1bpx5F1wO0yCxr1ozhltBPm8DESSuHH YdC6ATsE2AndG8QJAmF8cuCTeIksSluyELJvh7RY= Received: from localhost (i5E862C5E.versanet.de [94.134.44.94]) by mx.zohomail.com with SMTPS id 1660156784131221.60771061448702; Wed, 10 Aug 2022 11:39:44 -0700 (PDT) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> User-agent: mu4e 1.8.7; emacs 28.1 From: Ricardo Wurmus <rekado@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Date: Wed, 10 Aug 2022 20:25:00 +0200 In-reply-to: <87bktmtmol.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: <878rnwuemq.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: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@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: -1.0 (-) Ricardo Wurmus <rekado@HIDDEN> writes: > zimoun <zimon.toutoune@HIDDEN> writes: > >> At the cost of more bandwidth, we could switch from url-fetch to >> git-fetch. > > Let=E2=80=99s do it! I=E2=80=99m tired of Bioconductor archive shenaniga= ns messing with > package availability. I have finally taken the time to review this and implement a first draft of a change to the bioconductor importer and updater. There are some limitations: - 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 upstream= ) 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 switch= 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. Perhaps we could operate on the url included in the <upstream-source> instead of looking at the *current* package value. We=E2=80=99re only accessing =E2=80=9Cpackage=E2=80=9D once in the url-fetch case, so maybe = we can work around this problem. - 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 revi= sion counter in the version string. - the updater doesn=E2=80=99t work on version expressions like (git-version "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. - =E2=80=9Cexperiment=E2=80=9D or =E2=80=9Cdata=E2=80=9D packages are not k= ept 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. - the above exception means that we need to litter the importer and updater code with extra checks. With all these notes out of the way I=E2=80=99ll prepare a series of patches next. --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 18 Jul 2022 16:23:17 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jul 18 12:23:17 2022 Received: from localhost ([127.0.0.1]:51910 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oDTWe-0001sO-UT for submit <at> debbugs.gnu.org; Mon, 18 Jul 2022 12:23:17 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21149) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1oDTWa-0001sC-Bl for 39885 <at> debbugs.gnu.org; Mon, 18 Jul 2022 12:23:16 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1658161390; cv=none; d=zohomail.com; s=zohoarc; b=L4Za99exrEzRCpsUrDq1WoW9fYTGdH6kXedMrUtz37L6a4YZYtEBorMA/Hp4fttxDcw+iyI+MAteUyUstcsvMfpnFY//hvEYFuhRYAwMVB+Hp0Nn6JR0JPzlKeuwc3C3T7AifHwSUqqj+yYL5P4pF4GaznAKBKJkaSIHEvWiH0k= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1658161390; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=rDwB9hlLn6y3Ll9lcY0vgweAsUrgjRk7+iiUggPqo9o=; b=e7yBCzLYtd5MDvDiSruzw2hwP5ZcUzh5yYdrmMdO2w2bO1GkXuRQo6CPo8oSws2+CYP1/tkkg6upQFU5XceaVfv6Nu19POdzHZEOB6DCvWRzdyHiUa/UWRalcTwqlAX/m0maqW3xjozNDMXnt2rdYzf5N9+zamvtXP6zDXypdNw= 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=1658161390; 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=rDwB9hlLn6y3Ll9lcY0vgweAsUrgjRk7+iiUggPqo9o=; b=UFgA+0poJd9kw6PmWNE96kkLYIWIdv9QpVu5DLh02EzW0uYgSLSpPWBEKbMSj4cA oSytHfOLpwFJ3NHbe+Jc7UJAauGvFtYlp+wfipXmS5t+t6dqxBYETyCxRCUXCbhOvzZ THNyidiDYFTsWxImk8XSng9I3VOBqL0eWeZwuiOM= Received: from localhost (i5E862CB9.versanet.de [94.134.44.185]) by mx.zohomail.com with SMTPS id 1658161389855328.6619222096223; Mon, 18 Jul 2022 09:23:09 -0700 (PDT) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> User-agent: mu4e 1.6.11; emacs 28.1 From: Ricardo Wurmus <rekado@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Date: Mon, 18 Jul 2022 18:21:56 +0200 In-reply-to: <87lesqmmrr.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: <87bktmtmol.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: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@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: -1.0 (-) zimoun <zimon.toutoune@HIDDEN> writes: > At the cost of more bandwidth, we could switch from url-fetch to > git-fetch. Let=E2=80=99s do it! I=E2=80=99m tired of Bioconductor archive shenanigans= messing with package availability. --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
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From: zimoun <zimon.toutoune@HIDDEN>
To: 39885 <at> debbugs.gnu.org
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
Date: Mon, 18 Jul 2022 18:03:04 +0200
In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
(zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100")
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Hi,
Since 2020, I provided several examples of breakage with bug#39885 [1].
Here another one:
--8<---------------cut here---------------start------------->8---
$ guix time-machine --commit=77e2de365497bf4c8b81cbd78624f78293490485 \
-- build r-biocneighbors -S
substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
substitute: updating substitutes from 'https://bordeaux.guix.gnu.org'... 100.0%
The following derivation will be built:
/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv
building /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv...
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz...
download failed "https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz...
download failed "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://ci.guix.gnu.org/file/BiocNeighbors_1.4.1.tar.gz/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf...
download failed "https://ci.guix.gnu.org/file/BiocNeighbors_1.4.1.tar.gz/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://tarballs.nixos.org/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf...
download failed "https://tarballs.nixos.org/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://archive.softwareheritage.org/api/1/content/sha256:ae5d3f8d9a9ffd920cb94dc62d916c94b7e18632744c91e4e3489f21230b7117/raw/...
download failed "https://archive.softwareheritage.org/api/1/content/sha256:ae5d3f8d9a9ffd920cb94dc62d916c94b7e18632744c91e4e3489f21230b7117/raw/" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz...
download failed "https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" 404 "NOT FOUND"
Trying to use Disarchive to assemble /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz...
could not find its Disarchive specification
failed to download "/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz" from ("https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz")
builder for `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' failed to produce output path `/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz'
build of /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv failed
View build log at '/var/log/guix/drvs/q9/ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv.gz'.
guix build: error: build of `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' failed
--8<---------------cut here---------------end--------------->8---
Well, several comments:
1. Berlin or Bordeaux do not have it as substitutes,
2. Diasarchive does not have it,
3. Many others neither.
but the question in the first place is: why is Bioconductor failing?
Because they do ugly things!
Our history reads:
f431d5e299 Sun Dec 15 15:38:51 2019 +0100 guix: Upgrade to Bioconductor 3.10
12e2aa96dc Sun Dec 15 15:38:55 2019 +0100 gnu: r-biocneighbors: Update to 1.4.1.
aece78fe2f Sun Mar 1 23:38:12 2020 +0100 gnu: r-biocneighbors: Update to 1.4.2.
8e518d4802 Sat Jun 13 01:19:38 2020 +0200 guix: Update to Bioconductor 3.11.
which means that Bioconductor removes v1.4.1 from their URI scheme
(even, I do not know if the tarball is still available on their infra)
and despite the fact Bioconductor v3.10 had released v1.4.1, then it is
not stable.
At the cost of more bandwidth, we could switch from url-fetch to
git-fetch. Or we also could examine why Disarchive is failing here.
1: <http://issues.guix.gnu.org/issue/39885>
Cheers,
simon
bug-guix@HIDDEN:bug#39885; Package guix.
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From: zimoun <zimon.toutoune@HIDDEN>
To: 39885 <at> debbugs.gnu.org
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
Date: Mon, 22 Nov 2021 20:48:05 +0100
In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
(zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100")
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Hi,
On Tue, 03 Mar 2020 at 16:59, zimoun <zimon.toutoune@HIDDEN> wrote:
> Currently, the URI scheme (see 'bioconductor-uri' in
> guix/build-system/r.scm) is:
>
> https://bioconductor.org/packages/release/data/<type-url-part>/src/contr=
ib/<upstream-name>-<version>.tar.gz
>
> which leads to 2 issues:
>
> 1. when Bioconductor updates their release, some package versions are
> updated too, and so, the upstream return 404.
> 2. for this reason 1., the "guix time-machine" is broken for all the
> Bioconductor packages, at least if Berlin or SWH does not have a
> substitute; which is not expected for 'annotation' packages.
>
> However, the Bioconductor archive still serves the old release, i.e.,
>
> https://bioconductor.org/packages/3.x/data/<type-url-part>/src/contrib/<u=
pstream-name>-<version>.tar.gz
It is still the case and for concrete breakage, see [1]. I will not
detail but each time Guix lags behind Bioconductor new release, it is
broken. For sure, Guix upgrades more or less quickly. Each time
Bioconductor remove a package, it is broken. Well, because a lot
of care about R packages, the forward breakages happen barely. :-) But
backward breakages are not negligible, IMHO.
Well, this URL choice is not The Right Thing and somehow broken by design.
1: <https://issues.guix.gnu.org/39885#7>
> The ways to fix the both issues are:
>
> a) Add the Bioconductor release (known at packaging time) to all the
> packages; provide as argument to 'bioconductor-uri'.
> b) Add more URLs to fallback.
>
> As discussed on IRC, Tobias seems more inclined with the option a) and
> I am more in favour of option b.
>
> Attached, a quick patch showing the option b).
We are now 1.5 years after. And we did nothing; well we did other
things instead. ;-). Now, I have an strong opinion that option a) is
not doable: I speak using my janitor moves of Bioconductor packages.
Instead, something along the proposed patch below half-fixes the issue
now. We just have to append the releases and let the fallback mechanism
takes care. It reduces the maintenance burden, IMHO.
For sure, it is not perfect but it appears to me a pragmatical fix
waiting something better.
This better is unknown (at least from me :-)). On one hand Disarchive
would improve the situation for tarballs=E2=80=A6 but some work remains (ch=
eck
that SWH ingestion and rebuild is bullet-proof). On the other hand,
Bioconductor uses Git, for instance:
git clone https://git.bioconductor.org/packages/CATALYST
<https://bioconductor.org/packages/release/bioc/html/CATALYST.html>
And Bioconductor uses =E2=80=99origin/RELEASE_3.14=E2=80=99 as Git tag. Ba=
sed on this,
it would avoid the eternal inplace-change fixes.
For instance, the package tximeta [2], recently updated by Ricardo.
Well, from their Bioconductor Git repo,
git clone https://git.bioconductor.org/packages/tximeta
it is not clear that the current version is at 1.12.3. And it is not
clear either if they tagged origin/RELEASE_3_14 at 1.12.0 and did
something ugly to then get 1.12.3. Anyway, switch from url-fetch to
git-fetch is an option. However, it is as option a) and I am not
convinced it is doable with the resource at hand.
2: <https://bioconductor.org/packages/3.14/bioc/html/tximeta.html>
What could a plan to have a bullet-proof =E2=80=9Cguix time-machine=E2=80=
=9D for
Bioconductor?
Cheers,
simon
> From 87e73e02202fe5e342d68f1fb17efdd4425737cd Mon Sep 17 00:00:00 2001
> From: zimoun <zimon.toutoune@HIDDEN>
> Date: Tue, 3 Mar 2020 16:53:39 +0100
> Subject: [PATCH] build-system: r: Use Bioconductor old releases to fallba=
ck.
>
> * guix/build-system/r.scm (bioconductor-uri): Extend the fallback list.
> ---
> guix/build-system/r.scm | 21 ++++++++++++---------
> 1 file changed, 12 insertions(+), 9 deletions(-)
>
> diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
> index 2d328764b0..8638e1b888 100644
> --- a/guix/build-system/r.scm
> +++ b/guix/build-system/r.scm
> @@ -54,15 +54,18 @@ release corresponding to NAME and VERSION."
> ('annotation "/data/annotation")
> ('experiment "/data/experiment")
> (_ "/bioc"))))
> - (list (string-append "https://bioconductor.org/packages/release"
> - type-url-part
> - "/src/contrib/"
> - name "_" version ".tar.gz")
> - ;; TODO: use %bioconductor-version from (guix import cran)
> - (string-append "https://bioconductor.org/packages/3.10"
> - type-url-part
> - "/src/contrib/Archive/"
> - name "_" version ".tar.gz"))))
> + (append (list (string-append "https://bioconductor.org/packages/rele=
ase"
> + type-url-part
> + "/src/contrib/"
> + name "_" version ".tar.gz"))
> + (map (lambda (release)
> + (string-append "https://bioconductor.org/packages/"
> + release
> + type-url-part
> + "/src/contrib/"
> + name "_" version ".tar.gz"))
> + (list (@@ (guix import cran) %bioconductor-version)
> + "3.9" "3.8" "3.7")))))
>
> (define %r-build-system-modules
> ;; Build-side modules imported by default.
bug-guix@HIDDEN:bug#39885; Package guix.
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From: zimoun <zimon.toutoune@HIDDEN>
To: 39885 <at> debbugs.gnu.org
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
Date: Thu, 19 Nov 2020 15:22:11 +0100
In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
(zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100")
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Hi,
Some explanations of the issue are provided here:
<http://issues.guix.gnu.org/issue/39885>
Since we are currently updating to 3.12, maybe it is the occasion to fix
the issue. See option a) below.
On Tue, 03 Mar 2020 at 16:59, zimoun <zimon.toutoune@HIDDEN> wrote:
> Currently, the URI scheme (see 'bioconductor-uri' in
> guix/build-system/r.scm) is:
>
> https://bioconductor.org/packages/release/data/<type-url-part>/src/contr=
ib/<upstream-name>-<version>.tar.gz
>
> which leads to 2 issues:
>
> 1. when Bioconductor updates their release, some package versions are
> updated too, and so, the upstream return 404.
>
> 2. for this reason 1., the "guix time-machine" is broken for all the
> Bioconductor packages, at least if Berlin or SWH does not have a
> substitute; which is not expected for 'annotation' packages.
An example of this issue is for example:
--8<---------------cut here---------------start------------->8---
$ guix time-machine --commit=3Daee183e -- import cran -a bioconductor CATAL=
YST -r
Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.or=
g/git/guix.git'...
Starting download of /tmp/guix-file.Nxajqh
From https://bioconductor.org/packages/release/bioc/src/contrib/CATALYST_1.=
12.2.tar.gz...
download failed "https://bioconductor.org/packages/release/bioc/src/contrib=
/CATALYST_1.12.2.tar.gz" 404 "Not Found"
failed to download "/tmp/guix-file.Nxajqh" from "https://bioconductor.org/p=
ackages/release/bioc/src/contrib/CATALYST_1.12.2.tar.gz"
error: failed to retrieve package information from "https://cran.r-project.=
org/web/packages/CATALYST/DESCRIPTION": 404 ("Not Found")
Backtrace:
4 (primitive-load "/home/simon/.cache/guix/inferiors/vznc=E2=80=
=A6")
In guix/ui.scm:
2117:12 3 (run-guix-command _ . _)
In guix/scripts/import.scm:
120:11 2 (guix-import . _)
In srfi/srfi-1.scm:
586:17 1 (map1 (#f))
In guix/import/utils.scm:
258:2 0 (package->definition _)
guix/import/utils.scm:258:2: In procedure package->definition:
Throw to key `match-error' with args `("match" "no matching pattern" #f)'.
--8<---------------cut here---------------end--------------->8---
Aside the ugly backtrace which is tracked by #44115, the main issue is
because Bioconductor updated to 3.12 and Guix is still at 3.11.
Concretely, the issue is that =E2=80=99release=E2=80=99 in the URL:
<https://bioconductor.org/packages/release/bioc/src/contrib/CATALYST_1.12.2=
.tar.gz>
now refers to 3.12 (because Bioconductor update) and Guix still think it
is 3.11 (because Guix has not yet updated; work-in-progress). And
CATALYST in 3.12 is at version 1.14.0 against 1.12.2 for 3.11.
Therefore, the conflict and the error.
It means that while:
(define %bioconductor-version "3.11")
is not updated to 3.12, all the Bioconductor packages are broken; in the
meaning not buildable from source.
> a) Add the Bioconductor release (known at packaging time) to all the
> packages; provide as argument to 'bioconductor-uri'.
> b) Add more URLs to fallback, e.g.:
>
> https://bioconductor.org/packages/release/data/<type-url-part>/src/contri=
b/<upstream-name>-<version>.tar.gz
> https://bioconductor.org/packages/3.11/data/<type-url-part>/src/contrib/<=
upstream-name>-<version>.tar.gz
>
> Attached, a quick patch showing the option b).
Then each time we update Bioconductor, we add an URL to the list.
> As discussed on IRC, Tobias seems more inclined with the option a) and
> I am more in favour of option b.
Tobias and Ricardo are in favor for a) (see this thread). Which means a
lot of work IMHO, i.e., add 3.11 as arguments and then 3.12 to all the
Bioconductor packages and fix the importer, IIUC; while b) means do
nothing except merge the proposed patch (possibly re-worked).
Just to note that only the task to group in bioconductor.scm all the
Bioconductor packages scattered here and there is still not done, I
think option a) is not doable by hand =E2=80=93 I do not volunteer! :-) Els=
e,
any suggestion to script the task instead?
Since I am more in favor of b), I am less motivated to fix the a). ;-)
But I am motivated to fix the issue at hand. :-)
Other option c) is to switch all the Bioconductor to git-fetch instead
of url-fetch. I have not checked yet how could be the transition.
> Please also consider #36805 which was never merged or closed.
> http://issues.guix.gnu.org/issue/36805
This patch could help for option a).
WDYT?
All the best,
simon
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 29 Jun 2020 20:42:56 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jun 29 16:42:56 2020 Received: from localhost ([127.0.0.1]:49623 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jq0cC-0003zQ-4z for submit <at> debbugs.gnu.org; Mon, 29 Jun 2020 16:42:56 -0400 Received: from eggs.gnu.org ([209.51.188.92]:56408) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludo@HIDDEN>) id 1jq0c9-0003zC-V3 for 39885 <at> debbugs.gnu.org; Mon, 29 Jun 2020 16:42:54 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:38276) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from <ludo@HIDDEN>) id 1jq0c4-0005yQ-A3; Mon, 29 Jun 2020 16:42:48 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=46640 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from <ludo@HIDDEN>) id 1jq0c3-0002JI-PK; Mon, 29 Jun 2020 16:42:48 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> <87lfk7gd7d.fsf@HIDDEN> <CAJ3okZ36KrALgMq69zdkDsHcfMv09Lk=DPBmzW-4SePZPRAvnA@HIDDEN> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 12 Messidor an 228 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Mon, 29 Jun 2020 22:42:46 +0200 In-Reply-To: <CAJ3okZ36KrALgMq69zdkDsHcfMv09Lk=DPBmzW-4SePZPRAvnA@HIDDEN> (zimoun's message of "Mon, 29 Jun 2020 19:36:07 +0200") Message-ID: <87r1txa9ix.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39885 Cc: Ricardo Wurmus <rekado@HIDDEN>, 39885 <at> debbugs.gnu.org, Tobias Geerinckx-Rice <me@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: -3.3 (---) zimoun <zimon.toutoune@HIDDEN> skribis: > From c1c963a3b86e306a20c14626127e54d21843c22c Mon Sep 17 00:00:00 2001 > From: zimoun <zimon.toutoune@HIDDEN> > Date: Mon, 29 Jun 2020 19:18:20 +0200 > Subject: [PATCH] build-system/r: bioconductor-uri: Fix archive URL. > > * guix/build-system/r.scm (bioconductor-uri): Fix archive URL. Applied, thanks! I let the rest of you discuss the other issues. :-) Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 29 Jun 2020 17:36:29 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jun 29 13:36:29 2020 Received: from localhost ([127.0.0.1]:49368 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jpxhl-0003L2-AJ for submit <at> debbugs.gnu.org; Mon, 29 Jun 2020 13:36:29 -0400 Received: from mail-qk1-f177.google.com ([209.85.222.177]:33059) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1jpxhh-0003Kn-5s for 39885 <at> debbugs.gnu.org; Mon, 29 Jun 2020 13:36:27 -0400 Received: by mail-qk1-f177.google.com with SMTP id j80so16029715qke.0 for <39885 <at> debbugs.gnu.org>; Mon, 29 Jun 2020 10:36:25 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=8838tFRDuAOB4S8wBy/TixFHHxWd8OOaO/HiJIDDrkg=; b=l6E50j768qJ5/I4b+rsrNZqAqO6dSyw8CUbTb3B1wxo/0xQQdXmZpEDPHjC3aaJD6v EyhNwoYe8WtxafkCshH1LC0F6sCpQMSGEx0qLptgLANCW6eax2yo1d1cCKUFqz6bWWDh V6bz7MR0kysj89z+RJt9sdrJ+W7a8NdIk/FSHNMJnIQKp6qQVATMu7jxVUweZhpB7ANj ilusBtMzS3IZmvIZtrg8DL1zKQlLIBCqFAIqSEhbCL4bWhxI8VHAJgHj0HJbpkym7ZCq I5hRpOfbH+ob2J2ScE1SdXXw2D1Cstb4dQV8H4aRIcSVVaZnFCExKCNXDGXPolO3AXNG 2JZw== 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=8838tFRDuAOB4S8wBy/TixFHHxWd8OOaO/HiJIDDrkg=; b=ajI2qY9j1SAY+zM4NpCf1bZjkBhpVpshYdS/U+OquZZUHfN2DW66g4w4sVIP6EuQYM Uz52H5IcySTJq1l61plDO3XlXhEFMd8F3JWcBbbeaPqG1/94NYr6t5wP2BhfYjoE1/a2 aw43FJmPyDZfrtykZgae11tq8nZrJYi7jcfXyTijOsTIgjo2VQgFul6Li54MNVqG1wUT d8jfakgHX2xpNAYxEXGLUYfoN3uPPDmA3akss6StJOD5Aihrj9rxqVSyGGAkLvJGLJsw hDEB5MbKeInxqMvRaalKV/sFzQQeyx1XJHrI3tvaE5UXvgOcJH55g/c4RcVskvK01um7 2ERQ== X-Gm-Message-State: AOAM532E8mwbEbPUVz1IfHriJcDEA7tXw84b3cwbpa7lV0Zaa+2w1j52 9NTOnrh9Rh1YVKsgbKJ1k6eLE5mJkEqNqxRr5bg= X-Google-Smtp-Source: ABdhPJwuhjPLw0gdCi1UPHOkF1V47K6izRCl3Y77FztVienTNtfLzaknRlDjjpeQK09ldVWbHR+zDbVMBeJqvjBBvY8= X-Received: by 2002:a37:b847:: with SMTP id i68mr15888531qkf.126.1593452179449; Mon, 29 Jun 2020 10:36:19 -0700 (PDT) MIME-Version: 1.0 References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> <87lfk7gd7d.fsf@HIDDEN> In-Reply-To: <87lfk7gd7d.fsf@HIDDEN> From: zimoun <zimon.toutoune@HIDDEN> Date: Mon, 29 Jun 2020 19:36:07 +0200 Message-ID: <CAJ3okZ36KrALgMq69zdkDsHcfMv09Lk=DPBmzW-4SePZPRAvnA@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine To: =?UTF-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN> Content-Type: multipart/mixed; boundary="0000000000001f9a8e05a93c7f12" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39885 Cc: Ricardo Wurmus <rekado@HIDDEN>, 39885 <at> debbugs.gnu.org, Tobias Geerinckx-Rice <me@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: -1.0 (-) --0000000000001f9a8e05a93c7f12 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Ludo, On Sun, 28 Jun 2020 at 22:14, Ludovic Court=C3=A8s <ludo@HIDDEN> wrote: > Could you provide a patch for this? About the url, for sure, see attached. But it does not address the root of the problem. Well, I will try to find a slot and propose something. All the best, simon --0000000000001f9a8e05a93c7f12 Content-Type: text/x-patch; charset="US-ASCII"; name="0001-build-system-r-bioconductor-uri-Fix-archive-URL.patch" Content-Disposition: attachment; filename="0001-build-system-r-bioconductor-uri-Fix-archive-URL.patch" Content-Transfer-Encoding: base64 Content-ID: <f_kc0rske80> X-Attachment-Id: f_kc0rske80 RnJvbSBjMWM5NjNhM2I4NmUzMDZhMjBjMTQ2MjYxMjdlNTRkMjE4NDNjMjJjIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiB6aW1vdW4gPHppbW9uLnRvdXRvdW5lQGdtYWlsLmNvbT4KRGF0 ZTogTW9uLCAyOSBKdW4gMjAyMCAxOToxODoyMCArMDIwMApTdWJqZWN0OiBbUEFUQ0hdIGJ1aWxk LXN5c3RlbS9yOiBiaW9jb25kdWN0b3ItdXJpOiBGaXggYXJjaGl2ZSBVUkwuCgoqIGd1aXgvYnVp bGQtc3lzdGVtL3Iuc2NtIChiaW9jb25kdWN0b3ItdXJpKTogRml4IGFyY2hpdmUgVVJMLgotLS0K IGd1aXgvYnVpbGQtc3lzdGVtL3Iuc2NtIHwgMiArLQogMSBmaWxlIGNoYW5nZWQsIDEgaW5zZXJ0 aW9uKCspLCAxIGRlbGV0aW9uKC0pCgpkaWZmIC0tZ2l0IGEvZ3VpeC9idWlsZC1zeXN0ZW0vci5z Y20gYi9ndWl4L2J1aWxkLXN5c3RlbS9yLnNjbQppbmRleCBjOGVjOWFiZDBkLi41ZWY5ODJkNjZh IDEwMDY0NAotLS0gYS9ndWl4L2J1aWxkLXN5c3RlbS9yLnNjbQorKysgYi9ndWl4L2J1aWxkLXN5 c3RlbS9yLnNjbQpAQCAtNjEsNyArNjEsNyBAQCByZWxlYXNlIGNvcnJlc3BvbmRpbmcgdG8gTkFN RSBhbmQgVkVSU0lPTi4iCiAgICAgICAgICAgOzsgVE9ETzogdXNlICViaW9jb25kdWN0b3ItdmVy c2lvbiBmcm9tIChndWl4IGltcG9ydCBjcmFuKQogICAgICAgICAgIChzdHJpbmctYXBwZW5kICJo dHRwczovL2Jpb2NvbmR1Y3Rvci5vcmcvcGFja2FnZXMvMy4xMSIKICAgICAgICAgICAgICAgICAg ICAgICAgICB0eXBlLXVybC1wYXJ0Ci0gICAgICAgICAgICAgICAgICAgICAgICAgIi9zcmMvY29u dHJpYi9BcmNoaXZlLyIKKyAgICAgICAgICAgICAgICAgICAgICAgICAiL3NyYy9jb250cmliLyIK ICAgICAgICAgICAgICAgICAgICAgICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFyLmd6IikpKSkK IAogKGRlZmluZSAlci1idWlsZC1zeXN0ZW0tbW9kdWxlcwoKYmFzZS1jb21taXQ6IDZlYmYzMDA5 NTlhNThmZDFlZGE4NzUyMDVjNzVkMjExMzc4NjIyODUKLS0gCjIuMjYuMgoK --0000000000001f9a8e05a93c7f12--
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 28 Jun 2020 20:14:41 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Jun 28 16:14:41 2020 Received: from localhost ([127.0.0.1]:47019 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jpdhI-0004we-N7 for submit <at> debbugs.gnu.org; Sun, 28 Jun 2020 16:14:40 -0400 Received: from eggs.gnu.org ([209.51.188.92]:55892) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludo@HIDDEN>) id 1jpdhG-0004wM-6i for 39885 <at> debbugs.gnu.org; Sun, 28 Jun 2020 16:14:40 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:47195) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from <ludo@HIDDEN>) id 1jpdhA-0003Bu-Q6; Sun, 28 Jun 2020 16:14:32 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=42162 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from <ludo@HIDDEN>) id 1jpdhA-0007fh-FL; Sun, 28 Jun 2020 16:14:32 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 11 Messidor an 228 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Sun, 28 Jun 2020 22:14:30 +0200 In-Reply-To: <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> (zimoun's message of "Wed, 24 Jun 2020 13:07:13 +0200") Message-ID: <87lfk7gd7d.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39885 Cc: Ricardo Wurmus <rekado@HIDDEN>, 39885 <at> debbugs.gnu.org, Tobias Geerinckx-Rice <me@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: -3.3 (---) Hi, zimoun <zimon.toutoune@HIDDEN> skribis: > b) The fallback URI in guix/build-system/r.scm(bioconductor-uri) > added by commit c586f427b4831b9b492e5b900b2226e898b8fcfa is not > correct, if I do not misread: > > "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/GenomeGr= aphs_1.46.0.tar.gz" > 404 "Not Found" > > The correct seems to be (without Archive): > > https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeGraphs_1.46= .0.tar.gz Could you provide a patch for this? Thanks, Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 24 Jun 2020 11:07:33 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Jun 24 07:07:33 2020 Received: from localhost ([127.0.0.1]:37848 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jo3Fd-0003gC-6N for submit <at> debbugs.gnu.org; Wed, 24 Jun 2020 07:07:33 -0400 Received: from mail-qt1-f193.google.com ([209.85.160.193]:35378) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1jo3Fb-0003fz-0X for 39885 <at> debbugs.gnu.org; Wed, 24 Jun 2020 07:07:31 -0400 Received: by mail-qt1-f193.google.com with SMTP id z1so1326167qtn.2 for <39885 <at> debbugs.gnu.org>; Wed, 24 Jun 2020 04:07:31 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=Slqk+sBtPl9fPNSnQ7j0tNwurqWmGEnBR3I9Lv5v1vM=; b=XxlfNeoXbbaXVZetzoBj80Gb1GDFstyV/vFmnJBblZ1eTVXw5T+a/+LwZ6Ju7D56+d n+X79YtjVv0aHkuVC/vGZb+adyIxgUnX315ypUL0bwSXrpNXpzP/wyoJYG7uWX8ZA0bn DPb3ho9tgzU1ox4HwX2DsoaMcfHANNXjnrEi+W9FYV3ac0ayiicVCA3GVRvoffB1cmo5 rv6vi8AZAJlIB0i8E8KfouMXStsuGSQBM9X+tzGGVFcUzCQC+WJGftd37NeUROYcZa+I wUAU6gtyZBsp2WRN51h8rPxrUiFzELoczNyGH70hztZOe9n3cDmoju2AspO687WtWpf6 wWHA== 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; bh=Slqk+sBtPl9fPNSnQ7j0tNwurqWmGEnBR3I9Lv5v1vM=; b=ZAjknGAD0ag0SwS1U3gIF3DVeNZmbuQeG9cgIgIZqUEAwWnXxM2sFlb5hAV8z9b1BY Ax4g2uvOSKWWECsfvRweGsEP0kVp9A6D7DhbGtmBmGPDbgkfj2FczgevQ2iOpo5eP75q gwvTWmk78/hpKDoDCQ3ViIoLS1mW4XUy/HJDhhDbVfl80MHC2r9Ob9eyZL/m5wL9CdLh aiL96djCb059JBNvAPusGIR7AhsJR5HpBdeUdFuNVmd/3vx8DLuAF8x/o4i//cQbhRxz /Kn6iYVd0uRoHUXKlEWyJAq8wo3y1r+jvI8+clOZP+KmRehWGiPdEYyL2dy2+xZIUKXL 9MzA== X-Gm-Message-State: AOAM533m/hOsTr8/JR+rxoFejYJQkE3Xamb7n73gWnu9fRfGd/eTLMax GlXSx40AJU2XJXcA0V5a05h4/6YOqkxZbtJcsbiWYxxDH60= X-Google-Smtp-Source: ABdhPJyO6Hbb2ZLpgJN9lzKdOjCKbD5bMue1OUOHRlZUKA4tDb5A8ZTSAWzh5eV7KAtEB/AkpJd3EGaIHITsBrIX7C8= X-Received: by 2002:aed:3608:: with SMTP id e8mr26717302qtb.186.1592996844836; Wed, 24 Jun 2020 04:07:24 -0700 (PDT) MIME-Version: 1.0 References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> From: zimoun <zimon.toutoune@HIDDEN> Date: Wed, 24 Jun 2020 13:07:13 +0200 Message-ID: <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine To: 39885 <at> debbugs.gnu.org, Tobias Geerinckx-Rice <me@HIDDEN>, Ricardo Wurmus <rekado@HIDDEN> Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39885 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 (-) Dear, The time-machine is broken for some BioConductor packages.. For an example, consider the package "r-genomegraphs" which has been removed from the BioConductor in 3.11 release. (Well, now the issue is mitigated because ci.guix.gnu.org serves a lot of upstream substitutes but ci.guix.gnu.org could be down. Other said, we should use the upstream resources where they are available.) Concretely, there are 2 issues: a) What to do for the removed packages? For 3.11, the list is there [1]. Do we keep them in gnu/packages/bioconductor.scm but then 'bioconductor-uri' needs some tweaks? Or do we transfer them to the channel guix-past (for example)? b) The fallback URI in guix/build-system/r.scm(bioconductor-uri) added by commit c586f427b4831b9b492e5b900b2226e898b8fcfa is not correct, if I do not misread: --8<---------------cut here---------------start------------->8--- "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/GenomeGraphs_1.46.0.tar.gz" 404 "Not Found" --8<---------------cut here---------------end--------------->8--- The correct seems to be (without Archive): https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeGraphs_1.46.0.tar.gz All the best, simon 1: https://bioconductor.org/news/bioc_3_11_release/#deprecated-and-defunct-packages
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at submit) by debbugs.gnu.org; 21 May 2020 23:29:24 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu May 21 19:29:24 2020 Received: from localhost ([127.0.0.1]:57557 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jbucu-0002B4-47 for submit <at> debbugs.gnu.org; Thu, 21 May 2020 19:29:24 -0400 Received: from lists.gnu.org ([209.51.188.17]:52062) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1jbucs-0002Ax-Fa for submit <at> debbugs.gnu.org; Thu, 21 May 2020 19:29:22 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35370) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <zimon.toutoune@HIDDEN>) id 1jbucs-0008Cf-8k for bug-guix@HIDDEN; Thu, 21 May 2020 19:29:22 -0400 Received: from mail-qk1-x729.google.com ([2607:f8b0:4864:20::729]:39182) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from <zimon.toutoune@HIDDEN>) id 1jbucq-000650-Ku for bug-guix@HIDDEN; Thu, 21 May 2020 19:29:21 -0400 Received: by mail-qk1-x729.google.com with SMTP id w3so3553176qkb.6 for <bug-guix@HIDDEN>; Thu, 21 May 2020 16:29:20 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=wtsfHXo0CmcX4LU44eKI+QOxf+klOFvkaIdQR4MG89Y=; b=TkPtwSn3rsH1WZt/HhVRgMCxaLH/+w9fCAyoDUXtbQ9AcAdosXSs9byvZfXOiUOUsW mItV+gO7r49R6ZRXilGVKc8wv2GHhyjHSRlvNbHlojVz+iHXjpTRcDQGmpAm4yGrd2S3 Y2M/x7lyt954qJnHqorMuBXtaf1lHdGYd2dT6NtQ+wUEClb5W1jALkRKIJF+OD2HSt9z aFJPNcE2/mnstn6edPtlbKWnTgFcU3YZwWsM2GNBIxD2OpDf1n2SnsVJMpVmZ+NxoxYn tCUF2ox2FjwOsnQ68Y7j2oE97VBR9Cqyy/q2t6lqDAASfDz+cWPw7SrdueXUXleR7ta+ IfJQ== 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:content-transfer-encoding; bh=wtsfHXo0CmcX4LU44eKI+QOxf+klOFvkaIdQR4MG89Y=; b=PVozaQCnWC4dIeryyZy9l6Nw6BkytPhHQPhdGy6tWpGD+z9xVCIxNtfiFAm/vLvjbt 5Q8GbUUl/FUXk3qLTlQuqnFaFrJUsAJ8feEcRZDqmAAkvEA5HUSrcfJYKkivm2+B8uK2 Zd02/onxqvHN8VJXKsML5V6pXhWJayT+nNutcHUKAlKPZzhWV29bHET1UndcdijcfG+v CvFOexcJLhqafDxbYOD9JmFWB9EPFoLWN6T/atqxja8/MJtga/tGAz9CxE6Qyz6AKgB4 DVEWN3Dc/9FZtKiak0UGgMtKNoL6ZIJhnuu4J23OtYtRqJOV7IpqZlmbOARfbBWEOcB2 JhaQ== X-Gm-Message-State: AOAM531RdEOnpoiTlKeFaA5fBLZ6SRQoxSZSelgY7K5dt/3PHfPyMlaM uMlvg56bRU6W3LI7lEspKD7z+NPozKL6BChrQtQ= X-Google-Smtp-Source: ABdhPJyVbij/NfZ4xxArEkiRnCu1j4sfRcnvxdXI9tBHwSJuVfBVxVo5anyWkQeV4zJ0uH5dRzWNyojUO3jlsIogmeI= X-Received: by 2002:a05:620a:148a:: with SMTP id w10mr719359qkj.201.1590103759532; Thu, 21 May 2020 16:29:19 -0700 (PDT) MIME-Version: 1.0 References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87ftdylqdn.fsf@HIDDEN> In-Reply-To: <87ftdylqdn.fsf@HIDDEN> From: zimoun <zimon.toutoune@HIDDEN> Date: Fri, 22 May 2020 01:29:08 +0200 Message-ID: <CAJ3okZ1Ttjh+iG3qU1a_PcK_m5-64+KLAGKYT7b5Cum7fGgkKA@HIDDEN> Subject: Re: Bioconductor URI, fallback and time-machine To: Ricardo Wurmus <rekado@HIDDEN> Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=2607:f8b0:4864:20::729; envelope-from=zimon.toutoune@HIDDEN; helo=mail-qk1-x729.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. 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_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=_AUTOLEARN X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Tobias Geerinckx-Rice <me@HIDDEN>, 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 (--) Dear Ricardo, On Mon, 23 Mar 2020 at 22:21, Ricardo Wurmus <rekado@HIDDEN> wrote: > > a) Add the Bioconductor release (known at packaging time) to all the > > packages; provide as argument to 'bioconductor-uri'. > > b) Add more URLs to fallback. > > > > As discussed on IRC, Tobias seems more inclined with the option a) and > > I am more in favour of option b. > > I think option a) is more explicit, which is probably what we generally > want to future-proof the time-machine. Fallbacks are okay in the case > of the CRAN URL where it=E2=80=99s not necessarily clear when a package t= arball > moves from the release location to the archive. > > In the case of Bioconductor URLs it seems that we can afford to be a bit > more accurate. We are going for option a) which means rename all the URLs, right? Because it is a lot, I suggest to first address the bug#36805, i.e., provide as an argument the BioConductor version to 'bioconductor-uri' and applies this policy to all the new packages or any update of them. Moreover, I have suggested to reorganise bioconductor.scm, bioinformatics.scm, cran.scm, etc. and I have not dedicated enough time to this boring task. But because I am working remotely (semi-lockdown), I plan to work on it next week and so this change of URLs could be part of the big reorganisation. What do you think? [1] http://issues.guix.gnu.org/issue/36805 All the best, simon
bug-guix@HIDDEN:bug#39885; Package guix.
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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=1584998457; 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=n8NrkkNG/fHNgvYtRKhtjssxxEvyVaopQnSHXvx34dE=; b=i3vn69XpykUi2P7y54xdslnk30VEVJWPXhVHG6fCKtbzbtMJUEVas20Ut1H5JOC+ B+0OBWmmxGEqyiFAcQFtv1BiMSfpwHX6a33niCmGHxXUGEmXPdkAHezD3ALXvDj9Qax T00Ix/Bsx0HzwAi2t0dIfnmB7A0jjsL+YyxoCCsM= Received: from localhost (p54AD4C06.dip0.t-ipconnect.de [84.173.76.6]) by mx.zohomail.com with SMTPS id 158499845592892.48841001393998; Mon, 23 Mar 2020 14:20:55 -0700 (PDT) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus <rekado@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: Bioconductor URI, fallback and time-machine In-reply-to: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@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: Mon, 23 Mar 2020 22:20:52 +0100 Message-ID: <87ftdylqdn.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 136.143.188.51 X-Spam-Score: 0.3 (/) X-Debbugs-Envelope-To: submit Cc: Tobias Geerinckx-Rice <me@HIDDEN>, 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: -0.7 (/) zimoun <zimon.toutoune@HIDDEN> writes: > 1. when Bioconductor updates their release, some package versions are > updated too, and so, the upstream return 404. > 2. for this reason 1., the "guix time-machine" is broken for all the > Bioconductor packages, at least if Berlin or SWH does not have a > substitute; which is not expected for 'annotation' packages. > > However, the Bioconductor archive still serves the old release, i.e., > > https://bioconductor.org/packages/3.x/data/<type-url-part>/src/contrib/<u= pstream-name>-<version>.tar.gz > > > The ways to fix the both issues are: > > a) Add the Bioconductor release (known at packaging time) to all the > packages; provide as argument to 'bioconductor-uri'. > b) Add more URLs to fallback. > > As discussed on IRC, Tobias seems more inclined with the option a) and > I am more in favour of option b. I think option a) is more explicit, which is probably what we generally want to future-proof the time-machine. Fallbacks are okay in the case of the CRAN URL where it=E2=80=99s not necessarily clear when a package tar= ball moves from the release location to the archive. In the case of Bioconductor URLs it seems that we can afford to be a bit more accurate. --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at submit) by debbugs.gnu.org; 3 Mar 2020 15:59:21 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Mar 03 10:59:21 2020 Received: from localhost ([127.0.0.1]:39878 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1j99x2-0000FJ-UH for submit <at> debbugs.gnu.org; Tue, 03 Mar 2020 10:59:21 -0500 Received: from lists.gnu.org ([209.51.188.17]:55483) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99x0-0000FA-VN for submit <at> debbugs.gnu.org; Tue, 03 Mar 2020 10:59:19 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:51176) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99wz-00031a-KH for bug-guix@HIDDEN; Tue, 03 Mar 2020 10:59:18 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99wy-0004eG-3x for bug-guix@HIDDEN; Tue, 03 Mar 2020 10:59:17 -0500 Received: from mail-qv1-xf30.google.com ([2607:f8b0:4864:20::f30]:34213) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99wx-0004ds-T3 for bug-guix@HIDDEN; Tue, 03 Mar 2020 10:59:16 -0500 Received: by mail-qv1-xf30.google.com with SMTP id o18so1906342qvf.1 for <bug-guix@HIDDEN>; Tue, 03 Mar 2020 07:59:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=iBVlumUQoU0iu5kIlGcsDSeMtZQUgC9C48NqR/D85OY=; b=SWVrpEqfF2aB1utVLia3sZ+B44JDgBOpz39r9J5wrkMBha/bLLMxXlcR3x2Y1lYhKK yeg0iad4+lJi7raN/al0pW1JSfLOyCaEBci7MEmDuQ2HiTnPz8YW5KbmKK5YcgqU1zkM P5ukzP3VGHDu1CIM5RGDkgSZ4ysWCWusQoVedwuyz6II4JadCAKSDf4akG2DP4p22/UT 2Z0h/1MQoUw8iyA+1z239MEU6Q8Z16wQ5mhdHebozHWcvnfmJoo+LDNH6i4yw7ofG2g0 ODILzSRer0d66rsHB2VrS3yklpAezeoS92faLN35Zq575aTaHThXK+T0jx+KA1Kshu9j qbxg== 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; bh=iBVlumUQoU0iu5kIlGcsDSeMtZQUgC9C48NqR/D85OY=; b=nR8T9DK32NJT7FoD/agU4nq+g4feTvJztCmwt+uZGwMngbZaQzrwWr8Ij7MkXzhVGN 7sB7xYN3ldhf0VVtpbD19PfgYV24Ojr+sYQ/5VEoCZO6ISo8lpG88TF2Y0/oOXqv6IAf YAx2d+bfaFb0tjpAmP/BmoHjWmG0cLmWDPgx6k5HnetbV3yWmsaSwmIxV0hYTnp1VT7E ypFbR/ke+r8vvPNP8GxD0Ix2ZUGEvP3jQ1eBQiVW5yLjiuMRDPxkn2fnfdDRXGco2xQ6 GY0TYD6iM8z7KZPs7fltlOLooecBrwNnoCbBYioyTY/WHFIWtRztmCMem68OPaA7Z/6i gOow== X-Gm-Message-State: ANhLgQ2Z7ZnUW3yatQ0Tkv56PEfjkuc2/hdBj5bW2EbaUta7wyeiyIuj GpFeO5sjy/ecFeYJnWKnh9veXy/PSbn9/tZb+LvB5nqo X-Google-Smtp-Source: ADFU+vt4BmdA4UtrRMxkWt0vSOTQASTnc+TDTD+akngrfOIJ2NwFCm/TJPZSPWq9VDv77/05YSJvy2fThlOxOaV1Y7Q= X-Received: by 2002:ad4:4674:: with SMTP id z20mr4612454qvv.6.1583251154670; Tue, 03 Mar 2020 07:59:14 -0800 (PST) MIME-Version: 1.0 From: zimoun <zimon.toutoune@HIDDEN> Date: Tue, 3 Mar 2020 16:59:03 +0100 Message-ID: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> Subject: Bioconductor URI, fallback and time-machine To: bug-guix@HIDDEN, Tobias Geerinckx-Rice <me@HIDDEN>, Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/mixed; boundary="000000000000aa3660059ff5625d" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:4864:20::f30 X-Spam-Score: 0.3 (/) 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: -0.7 (/) --000000000000aa3660059ff5625d Content-Type: text/plain; charset="UTF-8" Dear, Currently, the URI scheme (see 'bioconductor-uri' in guix/build-system/r.scm) is: https://bioconductor.org/packages/release/data/<type-url-part>/src/contrib/<upstream-name>-<version>.tar.gz which leads to 2 issues: 1. when Bioconductor updates their release, some package versions are updated too, and so, the upstream return 404. 2. for this reason 1., the "guix time-machine" is broken for all the Bioconductor packages, at least if Berlin or SWH does not have a substitute; which is not expected for 'annotation' packages. However, the Bioconductor archive still serves the old release, i.e., https://bioconductor.org/packages/3.x/data/<type-url-part>/src/contrib/<upstream-name>-<version>.tar.gz The ways to fix the both issues are: a) Add the Bioconductor release (known at packaging time) to all the packages; provide as argument to 'bioconductor-uri'. b) Add more URLs to fallback. As discussed on IRC, Tobias seems more inclined with the option a) and I am more in favour of option b. Attached, a quick patch showing the option b). Please also consider #36805 which was never merged or closed. http://issues.guix.gnu.org/issue/36805 All the best, simon --000000000000aa3660059ff5625d Content-Type: text/x-patch; charset="US-ASCII"; name="0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch" Content-Disposition: attachment; filename="0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch" Content-Transfer-Encoding: base64 Content-ID: <f_k7c2u5mz0> X-Attachment-Id: f_k7c2u5mz0 RnJvbSA4N2U3M2UwMjIwMmZlNWUzNDJkNjhmMWZiMTdlZmRkNDQyNTczN2NkIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiB6aW1vdW4gPHppbW9uLnRvdXRvdW5lQGdtYWlsLmNvbT4KRGF0 ZTogVHVlLCAzIE1hciAyMDIwIDE2OjUzOjM5ICswMTAwClN1YmplY3Q6IFtQQVRDSF0gYnVpbGQt c3lzdGVtOiByOiBVc2UgQmlvY29uZHVjdG9yIG9sZCByZWxlYXNlcyB0byBmYWxsYmFjay4KCiog Z3VpeC9idWlsZC1zeXN0ZW0vci5zY20gKGJpb2NvbmR1Y3Rvci11cmkpOiBFeHRlbmQgdGhlIGZh bGxiYWNrIGxpc3QuCi0tLQogZ3VpeC9idWlsZC1zeXN0ZW0vci5zY20gfCAyMSArKysrKysrKysr KystLS0tLS0tLS0KIDEgZmlsZSBjaGFuZ2VkLCAxMiBpbnNlcnRpb25zKCspLCA5IGRlbGV0aW9u cygtKQoKZGlmZiAtLWdpdCBhL2d1aXgvYnVpbGQtc3lzdGVtL3Iuc2NtIGIvZ3VpeC9idWlsZC1z eXN0ZW0vci5zY20KaW5kZXggMmQzMjg3NjRiMC4uODYzOGUxYjg4OCAxMDA2NDQKLS0tIGEvZ3Vp eC9idWlsZC1zeXN0ZW0vci5zY20KKysrIGIvZ3VpeC9idWlsZC1zeXN0ZW0vci5zY20KQEAgLTU0 LDE1ICs1NCwxOCBAQCByZWxlYXNlIGNvcnJlc3BvbmRpbmcgdG8gTkFNRSBhbmQgVkVSU0lPTi4i CiAgICAgICAgICAgICAgICAgICAgICAgICAgKCdhbm5vdGF0aW9uICIvZGF0YS9hbm5vdGF0aW9u IikKICAgICAgICAgICAgICAgICAgICAgICAgICAoJ2V4cGVyaW1lbnQgIi9kYXRhL2V4cGVyaW1l bnQiKQogICAgICAgICAgICAgICAgICAgICAgICAgIChfICIvYmlvYyIpKSkpCi0gICAgKGxpc3Qg KHN0cmluZy1hcHBlbmQgImh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy9yZWxlYXNl IgotICAgICAgICAgICAgICAgICAgICAgICAgIHR5cGUtdXJsLXBhcnQKLSAgICAgICAgICAgICAg ICAgICAgICAgICAiL3NyYy9jb250cmliLyIKLSAgICAgICAgICAgICAgICAgICAgICAgICBuYW1l ICJfIiB2ZXJzaW9uICIudGFyLmd6IikKLSAgICAgICAgICA7OyBUT0RPOiB1c2UgJWJpb2NvbmR1 Y3Rvci12ZXJzaW9uIGZyb20gKGd1aXggaW1wb3J0IGNyYW4pCi0gICAgICAgICAgKHN0cmluZy1h cHBlbmQgImh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy8zLjEwIgotICAgICAgICAg ICAgICAgICAgICAgICAgIHR5cGUtdXJsLXBhcnQKLSAgICAgICAgICAgICAgICAgICAgICAgICAi L3NyYy9jb250cmliL0FyY2hpdmUvIgotICAgICAgICAgICAgICAgICAgICAgICAgIG5hbWUgIl8i IHZlcnNpb24gIi50YXIuZ3oiKSkpKQorICAgIChhcHBlbmQgKGxpc3QgKHN0cmluZy1hcHBlbmQg Imh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy9yZWxlYXNlIgorICAgICAgICAgICAg ICAgICAgICAgICAgICAgICAgICAgdHlwZS11cmwtcGFydAorICAgICAgICAgICAgICAgICAgICAg ICAgICAgICAgICAgIi9zcmMvY29udHJpYi8iCisgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFyLmd6IikpCisgICAgICAgICAgICAobWFwIChsYW1i ZGEgKHJlbGVhc2UpCisgICAgICAgICAgICAgICAgICAgKHN0cmluZy1hcHBlbmQgImh0dHBzOi8v YmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy8iCisgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICAgcmVsZWFzZQorICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgIHR5cGUtdXJs LXBhcnQKKyAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAiL3NyYy9jb250cmliLyIK KyAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFy Lmd6IikpCisgICAgICAgICAgICAgICAgIChsaXN0IChAQCAoZ3VpeCBpbXBvcnQgY3JhbikgJWJp b2NvbmR1Y3Rvci12ZXJzaW9uKQorICAgICAgICAgICAgICAgICAgICAgICAiMy45IiAiMy44IiAi My43IikpKSkpCiAKIChkZWZpbmUgJXItYnVpbGQtc3lzdGVtLW1vZHVsZXMKICAgOzsgQnVpbGQt c2lkZSBtb2R1bGVzIGltcG9ydGVkIGJ5IGRlZmF1bHQuCi0tIAoyLjI1LjAKCg== --000000000000aa3660059ff5625d--
zimoun <zimon.toutoune@HIDDEN>:bug-guix@HIDDEN.
Full text available.bug-guix@HIDDEN:bug#39885; Package guix.
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