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Mon, 08 Jan 2024 01:09:14 -0800 (PST) From: Simon Tournier In-Reply-To: <874jgacq4u.fsf_-_@gnu.org> References: <87lesqmmrr.fsf@gmail.com> <874jgacq4u.fsf_-_@gnu.org> Date: Mon, 08 Jan 2024 10:09:08 +0100 Message-ID: <87le9019aj.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-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Migadu-Scanner: mx13.migadu.com X-Migadu-Spam-Score: -5.19 X-Spam-Score: -5.19 X-Migadu-Queue-Id: A7A6439414 X-TUID: 9BRECr8C0em5 Hi, On Fri, 22 Dec 2023 at 14:40, Ludovic Court=C3=A8s wrote: >> guix build: error: build of `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv= -BiocNeighbors_1.4.1.tar.gz.drv' failed First thing first, please note that we are speaking about tag 1.4.1 and not 1.20.0. And this 1.4.1 is gone from =E2=80=9Cour=E2=80=9D infra since= =E2=80=A6 ?? That=E2=80=99s one of the things I do not like with Guix: I never know what to expect from the infra. Anyway, I have my list of TODOs for improving the annoyances (I and maybe others have :-)); stay tuned. ;-) Considering the state of =E2=80=9Cour=E2=80=9D infra and how Bioconductor m= anages the tarballs, many tarballs are lost forever, sadly. Although the content is still around, I guess. > I was wondering whether we=E2=80=99re now doing better for Bioconductor > tarballs. The answer, based on small sample, seems to be =E2=80=9Cnot qu= ite=E2=80=9D: Thanks for diving into this. > has entries like: > > --8<---------------cut here---------------start------------->8--- > { > "type": "url", > "urls": [ > "https://bioconductor.org/packages/release/bioc/src/contrib/BiocN= eighbors_1.20.0.tar.gz", > "https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeig= hbors_1.20.0.tar.gz", > "https://bordeaux.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/s= ha256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas", > "https://ci.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/sha256/= 0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas", > "https://tarballs.nixos.org/sha256/0a5wg099fgwjbzd6r3mr4l02rcmjql= kdcz1w97qzwx1mir41fmas" > ], > "integrity": "sha256-WlUXSI41dP7xSTx81ibFsrIsACW5jmzaX5I/lxJ4vCg=3D= ", > "outputHashAlgo": "sha256", > "outputHashMode": "flat" > }, > --8<---------------cut here---------------end--------------->8--- Please note that Bioconductor 3.18 released BiocNeighbors v1.20.0 but then updated to v1.20.1 still under Bioconductor 3.18 and Ricardo did this update with 5673484cbc2ed74c61ae81d623646fa7829fbc32. On a side note, between the Bioconductor update and the update on our side, there is a mismatch where the source of r-biocneighbors is unreachable. Other said, post-update on our side, --8<---------------cut here---------------start------------->8--- $ zcat sources.json | jq | grep BiocNeighbors | grep bioconductor | sed 's/= "//g' | sed 's/,//g' https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeig= hbors_1.20.1.tar.gz https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbo= rs_1.20.1.tar.gz $ for url in $(zcat sources.json | jq | grep BiocNeighbors | grep bioconduc= tor | sed 's/"//g' | sed 's/,//g'); \ do guix download $url ;done Starting download of /tmp/guix-file.STc9fQ >From https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbo= rs_1.20.1.tar.gz... =E2=80=A6_1.20.1.tar.gz 1015KiB = 60.3MiB/s 00:00 =E2=96=95=E2= =96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96= =88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88= =E2=96=88=E2=96=8F 100.0% /gnu/store/nxab1pskh9zcjspczph6jcs5fk79pb7k-BiocNeighbors_1.20.1.tar.gz 0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j Starting download of /tmp/guix-file.aZFRLv >From https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_= 1.20.1.tar.gz... =E2=80=A6_1.20.1.tar.gz 1015KiB = 63.5MiB/s 00:00 =E2=96=95=E2= =96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96= =88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88= =E2=96=88=E2=96=8F 100.0% /gnu/store/nxab1pskh9zcjspczph6jcs5fk79pb7k-BiocNeighbors_1.20.1.tar.gz 0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j --8<---------------cut here---------------end--------------->8--- but, now the past reads, --8<---------------cut here---------------start------------->8--- $ for url in https://bioconductor.org/packages/release/bioc/src/contrib/Bio= cNeighbors_1.20.0.tar.gz \ https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNe= ighbors_1.20.0.tar.gz ; \ do guix download $url ;done > >=20 Starting download of /tmp/guix-file.MUB3ow >From https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbo= rs_1.20.0.tar.gz... download failed "https://bioconductor.org/packages/release/bioc/src/contrib= /BiocNeighbors_1.20.0.tar.gz" 404 "Not Found" Starting download of /tmp/guix-file.MUB3ow >From https://web.archive.org/web/20240102105016/https://bioconductor.org/pa= ckages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz... download failed "https://web.archive.org/web/20240102105016/https://biocond= uctor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz" 40= 4 "NOT FOUND" Trying to use Disarchive to assemble /tmp/guix-file.MUB3ow... could not find its Disarchive specification failed to download "/tmp/guix-file.MUB3ow" from "https://bioconductor.org/p= ackages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz" guix download: error: https://bioconductor.org/packages/release/bioc/src/co= ntrib/BiocNeighbors_1.20.0.tar.gz: download failed Starting download of /tmp/guix-file.ZO9N08 >From https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_= 1.20.0.tar.gz... download failed "https://bioconductor.org/packages/3.18/bioc/src/contrib/Bi= ocNeighbors_1.20.0.tar.gz" 404 "Not Found" Starting download of /tmp/guix-file.ZO9N08 >From https://web.archive.org/web/20240102105018/https://bioconductor.org/pa= ckages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz... download failed "https://web.archive.org/web/20240102105018/https://biocond= uctor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz" 404 "= NOT FOUND" Trying to use Disarchive to assemble /tmp/guix-file.ZO9N08... could not find its Disarchive specification failed to download "/tmp/guix-file.ZO9N08" from "https://bioconductor.org/p= ackages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz" guix download: error: https://bioconductor.org/packages/3.18/bioc/src/contr= ib/BiocNeighbors_1.20.0.tar.gz: download failed --8<---------------cut here---------------end--------------->8--- As explained in [1], Bioconductor removes v1.20.0 from their URI scheme and despite the fact Bioconductor v3.18 had released v1.20.0, arf! And I do not even know if the tarball of v1.20.0 is kept on Bioconductor infra. Hum? Hence the discussion we had: switch from url-fetch to git-fetch. However, after some investigations, it does not seem straightforward: The main issue being the almost automatic current updater. See for details [2]. 1: bug#39885: Bioconductor URI, fallback and time-machine zimoun Mon, 18 Jul 2022 18:03:04 +0200 id:87lesqmmrr.fsf@gmail.com https://issues.guix.gnu.org/39885 https://issues.guix.gnu.org/msgid/87lesqmmrr.fsf@gmail.com https://yhetil.org/guix/87lesqmmrr.fsf@gmail.com 2: bug#39885: Bioconductor URI, fallback and time-machine Ricardo Wurmus Wed, 10 Aug 2022 20:25:00 +0200 id:878rnwuemq.fsf@elephly.net https://issues.guix.gnu.org/39885 https://issues.guix.gnu.org/msgid/878rnwuemq.fsf@elephly.net https://yhetil.org/guix/878rnwuemq.fsf@elephly.net > Any volunteer to write a script that=E2=80=99d generate a list of Biocond= uctor > content-addressed URLs (the bordeaux.guix.gnu.org/file ones) for say the > past couple of years? I did stuff past week about that. I will report this week what I did. Cheers, simon