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[194.254.61.44]) by smtp.gmail.com with ESMTPSA id bu19-20020a056000079300b0033d3d9447e3sm5973401wrb.83.2024.02.19.12.41.33 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 19 Feb 2024 12:41:33 -0800 (PST) From: Simon Tournier In-Reply-To: <87y1bkwfly.fsf@ngyro.com> References: <87lesqmmrr.fsf@gmail.com> <874jgacq4u.fsf_-_@gnu.org> <8734utba2a.fsf@ngyro.com> <87wmr7kr23.fsf@gmail.com> <87y1bkwfly.fsf@ngyro.com> Date: Mon, 19 Feb 2024 17:50:59 +0100 Message-ID: <87v86k4cuk.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-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Scanner: mx10.migadu.com X-Migadu-Spam-Score: 0.99 X-Spam-Score: 0.99 X-Migadu-Queue-Id: 84ECE21606 X-TUID: RQWq1MMJ8KUv Hi, On ven., 16 f=C3=A9vr. 2024 at 10:14, Timothy Sample wr= ote: >> Can we consider that this report is now done? Because: >> >> 1. SWH supports ExtID and nar hash lookup. >> >> 2. Missing origins are currently ingested by SWH. >> (via specific sources.json) > > I think that would be jumping the gun a little bit. > > In some sense, the report is only *done* when =E2=80=9Cstored=E2=80=9D hi= ts 100% (or > close to it, with the remainder being stuff we are pretty sure no longer > exists). This won=E2=80=99t happen just because of your second point the= re. Just to be sure: we are speaking about Bioconductor only, right? > When the historical =E2=80=9Csources.json=E2=80=9D is loaded, things will= be much, much, > better, sure. Sources will still be missing, though. Yeah, sources will still be missing but I expect that Bioconductor will be not. The only issue is about =E2=80=9Cannotation=E2=80=9D and maybe =E2= =80=9Cexperiment=E2=80=9D. However, here we are hitting the boundary between code and data: annotation and experiment might be very large and potentially skipped by SWH and they contain few if no code but plain data. We can still discuss what to do here; in this already long thread. :-) Or we can open another thread for this specific case about Bioconductor annotation and experiment. > To me, this is an > invitation to more subtle analysis, like weighing sources by their > =E2=80=9Cimportance=E2=80=9D in the package graph. Then there=E2=80=99s = still shortcomings with > Disarchive that have to be resolved (which is work best guided by > numbers in the report). Yeah. But that seems a large scope than Bioconductor case, no? > Also, it will always be a good idea to verify that things are working. > Ideally this could be simpler (leveraging ExtID lookup) and continuous. Indeed, checking that all Bioconductor sources can be extracted from SWH+Disarchive seems the path forward closing this report. :-) Cheers, simon