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In-reply-to: <436d649127861cd5e0f642551ece6729ed7500cb.camel@gnu.org> 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: Thu, 10 Sep 2020 12:38:41 +0200 Message-ID: <87k0x16hn2.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Received-SPF: pass client-ip=136.143.188.51; envelope-from=rekado@elephly.net; helo=sender4-of-o51.zoho.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/09/10 06:37:33 X-ACL-Warn: Detected OS = Linux 3.11 and newer [fuzzy] 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, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H2=-0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: guix-devel@gnu.org, guix-commits@gnu.org Errors-To: guix-devel-bounces+larch=yhetil.org@gnu.org Sender: "Guix-devel" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=elephly.net header.s=zoho header.b=aq1bF8d0; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-devel-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-devel-bounces@gnu.org X-Spam-Score: 1.99 X-TUID: Lt3GQAW5AKkO Roel Janssen writes: >> > commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea >> > Author: Roel Janssen >> > AuthorDate: Wed Sep 9 16:56:02 2020 +0200 >> >=20 >> > gnu: Add r-loomr. >> >=20=20=20=20=20 >> > * gnu/packages/bioinformatics.scm (r-loomr): New variable. >>=20 >> This is not free software. See >>=20 >> https://github.com/mojaveazure/loomR/pull/24 > > > Oh shoot. I'm sorry I didn't see this discussion! It=E2=80=99s really not obvious. I know because it happened to me too. In= 2018 I added r-loomr with commit fab43c6b84635200070c708d4220132be18dd239. Then in 2019 I removed it with commit bc70516bbae8a6388f3ed19008d3e10efd1577a7 after noticing that the author only used GPL in the DESCRIPTION file to stop the CRAN tools from complaining. It=E2=80=99s definitely unusual and very easy to miss. >> Aside from this, I would like to say two things: >>=20 >> > gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ >>=20 >> Let=E2=80=99s please not add R packages to (gnu packages bioinformatics)= when >> it >> can be avoided. (In this case there=E2=80=99s no CRAN package, so it=E2= =80=99s >> fine.) > > Where would I add a non-CRAN and non-Bioconductor package to? Perhaps > this situation won't occur again, and should raise a flag, because I > think I've never had this case before. We don=E2=80=99t have any good place for those packages. It would be good = to have a dumping ground for packages like that, and for those that are on CRAN but unusually depend on Bioconductor packages. > I will default to submitting patches to guix-patches again. I thought > it was trivial enough to just push. My mistake. I=E2=80=99d say if it=E2=80=99s on CRAN you can go ahead and push directly = (after running =E2=80=9Cguix lint=E2=80=9D to catch some obvious mistakes). Bioco= nductor packages need a little extra care because they are sometimes playing loose with licenses and included third-party code; but if you feel you=E2=80=99ve checked things carefully then you can also push those direct= ly. For third-party R packages we don=E2=80=99t benefit from even the little bi= t of quality control that CRAN and Bioconductor impose, so we need to be extra careful. There it helps to send patches to guix-patches and push them after some time. --=20 Ricardo