From mboxrd@z Thu Jan 1 00:00:00 1970 From: Giovanni Biscuolo Subject: [OT] Re: Guix and Bioconductor. Date: Sat, 21 Dec 2019 11:06:22 +0100 Message-ID: <871rsy6li9.fsf@roquette.mug.biscuolo.net> References: <87pnlz9lro.fsf@elephly.net> <877e869t80.fsf@elephly.net> <87k16si685.fsf@nckx> <87h81whxmw.fsf@nckx> <87fthf6wk7.fsf@roquette.mug.biscuolo.net> <875zibqczb.fsf@elephly.net> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:36916) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iiber-00057h-3L for guix-devel@gnu.org; Sat, 21 Dec 2019 05:06:50 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iibeo-0004bw-VT for guix-devel@gnu.org; Sat, 21 Dec 2019 05:06:48 -0500 Received: from ns13.heimat.it ([46.4.214.66]:58528) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1iibeo-0004Ru-IA for guix-devel@gnu.org; Sat, 21 Dec 2019 05:06:46 -0500 In-Reply-To: <875zibqczb.fsf@elephly.net> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ricardo Wurmus Cc: guix-devel@gnu.org --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable [A quick and dirty off topic rant... forgive me!] Hello Ricardo, thank you for the info! ...and thank you all for working on resolving this class of problems through Guix! Ricardo Wurmus writes: > Giovanni Biscuolo writes: [...] >> I fear flowPeacks will not be the last package with this kind licensing >> problems > > It sure isn=E2=80=99t. In the past I have tried to do a mass import from > Bioconductor and what slows me down the most is incorrect or non-free > licensing. There are some packages that declare to be licensed under > Artistic 2.0, but then actually they contain data from databases that > do not permit commercial use. Or they contain a copy of non-free tools, > or only work when those tools are present (e.g. kent tools, of which we > provide a package containing the few free tools). This confirms that licensing is an integral part of reproducibility and replicability, unfortunately a very neglected part even in academia (not to mention "industry") :-( . This is also part of the current science crisis... OK stop ranting :-D > It=E2=80=99s a pretty frustrating process to weed out these packages. Let them know! (Do they know?) =C2=ABDear Bioconductor Team, you state you are committed to bla bla reproducible research but *some* of the research you host is unreproducible for the simple reason some authors are ignoring licensing issues...=C2=BB >> Since =C2=ABBioconductor is committed to open source, collaborative, >> distributed software development and literate, reproducible research.=C2= =BB [1] > > CRAN appears to be stricter about licenses (even though =E2=80=9Cstrict= =E2=80=9D is > probably much too strong a word=E2=80=A6). Bioconductor people appear to= care a > little less. I'm out from academia, but every time I talk to friends involved in academia I'm pretty astonished by the general lack of scientific method [1] [2] applied in academia :-O. A little bit of metascience would help. ...and more Guix in academia is part of the solution :-D Thanks! Gio' [1] https://en.wikipedia.org/wiki/Reproducibility#Reproducible_research =C2=ABIn 2016, Nature conducted a survey of 1,576 researchers who took a brief online questionnaire on reproducibility in research. According to the survey, more than 70% of researchers have tried and failed to reproduce another scientist's experiments, and more than half have failed to reproduce their own experiments.=C2=BB [2] https://en.wikipedia.org/wiki/Replication_crisis =2D-=20 Giovanni Biscuolo Xelera IT Infrastructures --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEERcxjuFJYydVfNLI5030Op87MORIFAl397p4ACgkQ030Op87M ORJNWg/7BlPWazhR5PqEtmuHswV0E4qmuYasykrS4p/Zb3WMzEVxzHy7PTlqB3+e 6vxQ2fbMXewyy5Kh3ctM8mDZSL6/DUGKJKd/7NFxTUpz1IXhOZmf/+mDFak9v2BS s74E1YNY17fExRbHW+RVi4MvofLPAYnZ4+dCH8QGU8BNNXE4b3FMpfcJPfZ4HUkr G/ZjsAJH+MynnEJiyjzehbjX3ZZMU44lELJIrae2GCIQEtzGqExJGH8mDDNRBepi LFy1/aqQ9L/4WuD3rS1MaAzyPRcrTmnErM4LsSXSpMZ2DhF1x4SpQQH+9pHV+6OQ 9cC0I4UDfVOntyvQmBQgLh58zr1Iq9AiK4TnvpYO5t4Rsu+0qmHu0y0zri5c0DN3 4D+tOBdkfasdlHtSjLY403f3DilLZXg43bS44F4MwKZEUOkV18HgmUQSWcn/2D4p PbIhYJ9lCcDfQfFAzZD7ZR5+mXid6Oly2j+btJu1r3yrI/usUbzP/tyEnNiosfs6 EJzfRVXDCrQOjnNER0vhiMP65uNB6suVPuomAeCx0hS7Tp+1CH9nFH1AaURDEvOI hJMYbFN14FdgqoJ7QBNy89xUYZP63gRCXx5tdggEtkcYAvcfZD7QD5nftR8DGCr8 xAQGogYzfGxYbt4edGHUqzaQIkDkvT/KVjdIrLvMAwKPcNlEcs8= =5w3M -----END PGP SIGNATURE----- --=-=-=--