From unknown Sun Jun 22 11:37:29 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#28946 <28946@debbugs.gnu.org> To: bug#28946 <28946@debbugs.gnu.org> Subject: Status: licence problem with cufflinks Reply-To: bug#28946 <28946@debbugs.gnu.org> Date: Sun, 22 Jun 2025 18:37:29 +0000 retitle 28946 licence problem with cufflinks reassign 28946 guix submitter 28946 Dave Love severity 28946 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Sun Oct 22 12:52:58 2017 Received: (at submit) by debbugs.gnu.org; 22 Oct 2017 16:52:58 +0000 Received: from localhost ([127.0.0.1]:56134 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6JUg-0003Z9-Iq for submit@debbugs.gnu.org; Sun, 22 Oct 2017 12:52:58 -0400 Received: from eggs.gnu.org ([208.118.235.92]:58100) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6JUf-0003Yu-03 for submit@debbugs.gnu.org; Sun, 22 Oct 2017 12:52:57 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e6JUZ-0002q2-4J for submit@debbugs.gnu.org; Sun, 22 Oct 2017 12:52:51 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:47215) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1e6JUZ-0002pw-0t for submit@debbugs.gnu.org; Sun, 22 Oct 2017 12:52:51 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:49071) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1e6JUX-0000Bu-Ss for bug-guix@gnu.org; Sun, 22 Oct 2017 12:52:50 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1e6JUT-0002nz-36 for bug-guix@gnu.org; Sun, 22 Oct 2017 12:52:49 -0400 Received: from probity.mcc.ac.uk ([130.88.200.94]:13094) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1e6JUS-0002nY-St for bug-guix@gnu.org; Sun, 22 Oct 2017 12:52:45 -0400 Received: from asmtp2.its.manchester.ac.uk ([130.88.13.150]) by probity.mcc.ac.uk with esmtps (TLSv1:DHE-RSA-AES256-SHA:256) (Exim 4.85 (FreeBSD)) (envelope-from ) id 1e6JUR-000GQP-Hz for bug-guix@gnu.org; Sun, 22 Oct 2017 17:52:43 +0100 Received: from albion.it.manchester.ac.uk ([130.88.138.79]:48982) by asmtp2.its.manchester.ac.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (Exim 4.89) (envelope-from ) id 1e6JUR-0005bm-8o for bug-guix@gnu.org; Sun, 22 Oct 2017 17:52:43 +0100 From: Dave Love To: bug-guix@gnu.org Subject: licence problem with cufflinks Date: Sun, 22 Oct 2017 17:52:42 +0100 Message-ID: <87y3o3i0px.fsf@albion.it.manchester.ac.uk> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux) X-Draft-From: ("Misc" 3552) MIME-Version: 1.0 Content-Type: text/plain X-Authenticated-Sender: David Love from albion.it.manchester.ac.uk [130.88.138.79]:48982 X-Authenticated-From: Dave.Love@manchester.ac.uk X-SA-Exim-Connect-IP: 130.88.13.150 X-SA-Exim-Mail-From: fx@gnu.org X-SA-Exim-Scanned: No (on probity.mcc.ac.uk); SAEximRunCond expanded to false X-detected-operating-system: by eggs.gnu.org: FreeBSD 9.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) I noticed that there's a package for cufflinks, but it has a non-free component. It isn't packaged for Debian or Fedora because of that. See . From debbugs-submit-bounces@debbugs.gnu.org Sun Oct 22 17:40:10 2017 Received: (at 28946) by debbugs.gnu.org; 22 Oct 2017 21:40:11 +0000 Received: from localhost ([127.0.0.1]:56308 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6NyW-00062m-6v for submit@debbugs.gnu.org; Sun, 22 Oct 2017 17:40:10 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21031) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6NyT-00062J-V8 for 28946@debbugs.gnu.org; Sun, 22 Oct 2017 17:40:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1508708355; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; l=1460; bh=c1MskIUDaZHqq33Y+pNwBQ33FKT9RvZMY1NmjY5iiL8=; b=YFTmqkKjK78hUHyhRSck0nAHB0HjZWn+xNGmgcBYN3z3tO1JNqp+nK4RvkbuNlBD cq3copV0RFQHD3yQ0ogfmMH8yD0uxDSHBnKhICPgabnQ0rUADd6TsX7OiNXPjZZ0404 j2vwclG8j8fUjJrHa/iWuplcOhBWZ6Fl6bhHEAjA= Received: from localhost (port-92-200-48-141.dynamic.qsc.de [92.200.48.141]) by mx.zohomail.com with SMTPS id 1508708354995830.6056217728143; Sun, 22 Oct 2017 14:39:14 -0700 (PDT) References: <87y3o3i0px.fsf@albion.it.manchester.ac.uk> User-agent: mu4e 0.9.18; emacs 25.3.1 From: Ricardo Wurmus To: Dave Love Subject: Re: bug#28946: licence problem with cufflinks In-reply-to: <87y3o3i0px.fsf@albion.it.manchester.ac.uk> 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: Sun, 22 Oct 2017 23:39:11 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Message-ID: <87sheauakg.fsf@elephly.net> X-ZohoMailClient: External X-Spam-Score: -2.8 (--) X-Debbugs-Envelope-To: 28946 Cc: 28946@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.8 (--) Hi Dave, > I noticed that there's a package for cufflinks, but it has a non-free > component. It isn't packaged for Debian or Fedora because of that. See > . Thank you for the information! I=E2=80=99m going to investigate this. I downloaded an original release of C locfit from http://web.archive.org/web/20070616194305/http://cm.bell-labs.com/cm/ms= /departments/sia/project/locfit/dist/locfit.tgz and compared it to the copy in the Cufflinks repository at commit d402b182fabd9a831ccb4173e3cb3a2d2dd2e75e (May 2011). After copying a couple of files from src-c to src they do seem rather similar, but with about a thousand lines worth of differences (excluding whitespace changes). However, it doesn=E2=80=99t look like the code is bas= ed on any of the GPL versions on CRAN[1], because the archives there do not contain certain files (such as =E2=80=9Car_funs.c=E2=80=9D). If we could be reasonably sure that the code is a derivative of the GPL=E2=80=99d locfit code from CRAN we essentially deal with a GPL violatio= n, and not a case of non-free software. I=E2=80=99ll review this problem and will remove cufflinks by the end of th= is if we come to the conclusion that it cannot be considered free. [1]: https://cran.r-project.org/src/contrib/Archive/locfit/ -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 24 03:11:32 2017 Received: (at 28946) by debbugs.gnu.org; 24 Oct 2017 07:11:32 +0000 Received: from localhost ([127.0.0.1]:58350 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6tN3-0008G1-3j for submit@debbugs.gnu.org; Tue, 24 Oct 2017 03:11:32 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21054) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6tN1-0008Ft-Ql for 28946@debbugs.gnu.org; Tue, 24 Oct 2017 03:11:28 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1508829054; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; l=747; bh=JoKYincq6YJc7/6gsNeyk8mH3gE5gGg5VDQ3kk03UYg=; b=YgykNUyKvbn7ktgRSbzcUr7IIabJlNo88p83sO9RclvQa7M5BY++N+OJ/wfo6Il0 hbXh9xY9m9M7xeB9ZKtWlqE8z/grjEKEP6kgTJPyuJToRMFvgjYNdZQYbsPPROFJHQK ie/jzEbfUdEkUi1KJNO8ZmbBpPnSgbo30ikNuWt0= Received: from localhost (port-92-200-217-57.dynamic.qsc.de [92.200.217.57]) by mx.zohomail.com with SMTPS id 150882905458170.36872873624725; Tue, 24 Oct 2017 00:10:54 -0700 (PDT) References: <87y3o3i0px.fsf@albion.it.manchester.ac.uk> <87sheauakg.fsf@elephly.net> User-agent: mu4e 0.9.18; emacs 25.3.1 From: Ricardo Wurmus To: Dave Love Subject: Re: bug#28946: licence problem with cufflinks In-reply-to: <87sheauakg.fsf@elephly.net> 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: Tue, 24 Oct 2017 09:10:51 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Message-ID: <87wp3lc96s.fsf@mdc-berlin.de> X-ZohoMailClient: External X-Spam-Score: -2.8 (--) X-Debbugs-Envelope-To: 28946 Cc: 28946@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.8 (--) Ricardo Wurmus writes: > Hi Dave, > >> I noticed that there's a package for cufflinks, but it has a non-free >> component. It isn't packaged for Debian or Fedora because of that. See >> . > > Thank you for the information! I=E2=80=99m going to investigate this. [=E2=80=A6] I have written email to coletrap@uw.edu to report my findings and ask about details. > I=E2=80=99ll review this problem and will remove cufflinks by the end of = this if > we come to the conclusion that it cannot be considered free. That=E2=80=99s still what I intend to do. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 24 06:03:12 2017 Received: (at 28946) by debbugs.gnu.org; 24 Oct 2017 10:03:12 +0000 Received: from localhost ([127.0.0.1]:58384 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6w39-0004M7-Ux for submit@debbugs.gnu.org; Tue, 24 Oct 2017 06:03:12 -0400 Received: from serenity.mcc.ac.uk ([130.88.200.93]:12152) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e6w37-0004Lw-Bf for 28946@debbugs.gnu.org; Tue, 24 Oct 2017 06:03:06 -0400 Received: from asmtp2.its.manchester.ac.uk ([130.88.13.150]) by serenity.mcc.ac.uk with esmtps (TLSv1:DHE-RSA-AES256-SHA:256) (Exim 4.85 (FreeBSD)) (envelope-from ) id 1e6w35-000PAg-TB; Tue, 24 Oct 2017 11:03:03 +0100 Received: from albion.it.manchester.ac.uk ([130.88.138.79]:45492) by asmtp2.its.manchester.ac.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES256-GCM-SHA384:256) (Exim 4.89) (envelope-from ) id 1e6w35-0006wZ-Hi; Tue, 24 Oct 2017 11:03:03 +0100 From: Dave Love To: Ricardo Wurmus Subject: Re: bug#28946: licence problem with cufflinks References: <87y3o3i0px.fsf@albion.it.manchester.ac.uk> <87sheauakg.fsf@elephly.net> <87wp3lc96s.fsf@mdc-berlin.de> X-Draft-From: ("Misc" 3596) Date: Tue, 24 Oct 2017 11:03:02 +0100 In-Reply-To: <87wp3lc96s.fsf@mdc-berlin.de> (Ricardo Wurmus's message of "Tue, 24 Oct 2017 09:10:51 +0200") Message-ID: <87zi8ghnhl.fsf@albion.it.manchester.ac.uk> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Authenticated-Sender: David Love from albion.it.manchester.ac.uk [130.88.138.79]:45492 X-Authenticated-From: Dave.Love@manchester.ac.uk X-SA-Exim-Connect-IP: 130.88.13.150 X-SA-Exim-Mail-From: fx@gnu.org X-SA-Exim-Scanned: No (on serenity.mcc.ac.uk); SAEximRunCond expanded to false X-Spam-Score: -5.0(?) X-Spam-Flag: NO X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: 28946 Cc: 28946@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.3 (-) Ricardo Wurmus writes: > Ricardo Wurmus writes: > >> Hi Dave, >> >>> I noticed that there's a package for cufflinks, but it has a non-free >>> component. It isn't packaged for Debian or Fedora because of that. See >>> . >> >> Thank you for the information! I=E2=80=99m going to investigate this. > [=E2=80=A6] > > I have written email to coletrap@uw.edu to report my findings and ask > about details. Sorry, I could probably have saved you effort. I think I already mailed before cufflinks moved to github, and I also tried to track down the author of the problematic component, though they probably wouldn't hold the copyright as far as I remember.. From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 31 05:06:57 2017 Received: (at 28946-done) by debbugs.gnu.org; 31 Oct 2017 09:06:57 +0000 Received: from localhost ([127.0.0.1]:43199 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e9SVV-0004pj-Eu for submit@debbugs.gnu.org; Tue, 31 Oct 2017 05:06:55 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21091) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1e9SVT-0004pZ-Pu for 28946-done@debbugs.gnu.org; Tue, 31 Oct 2017 05:06:48 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1509434354; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; l=1234; bh=kEh2goxMXVW8pugCz77tB/3AgLMZigm/XdW75Ea68bE=; b=L21VPwomNdhkMsKmcsL/lQ+QjAMZYy8fh9O7CzT4tCW8N3U+Yqi3gPA6bWvTeY6i YbBiWJDYKsz+9xiRzLfNqveQ7H5AFwLEFKCmInAXwaHH1LKhj9d61t+3g23QCjT59a9 cZUfJl+gznvxQySma4XszENMRtnBqtnTX5kucypw= Received: from localhost (port-92-200-154-240.dynamic.qsc.de [92.200.154.240]) by mx.zohomail.com with SMTPS id 1509434353939190.9861357229978; Tue, 31 Oct 2017 00:19:13 -0700 (PDT) References: <87y3o3i0px.fsf@albion.it.manchester.ac.uk> <87sheauakg.fsf@elephly.net> <87wp3lc96s.fsf@mdc-berlin.de> <87zi8ghnhl.fsf@albion.it.manchester.ac.uk> User-agent: mu4e 0.9.18; emacs 25.3.1 From: Ricardo Wurmus To: Dave Love Subject: Re: bug#28946: licence problem with cufflinks In-reply-to: <87zi8ghnhl.fsf@albion.it.manchester.ac.uk> 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: Tue, 31 Oct 2017 08:19:10 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Message-ID: <8760avlr81.fsf@elephly.net> X-ZohoMailClient: External X-Spam-Score: -2.8 (--) X-Debbugs-Envelope-To: 28946-done Cc: 28946-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.8 (--) Dave Love writes: > Ricardo Wurmus writes: > >> Ricardo Wurmus writes: >> >>> Hi Dave, >>> >>>> I noticed that there's a package for cufflinks, but it has a non-free >>>> component. It isn't packaged for Debian or Fedora because of that. S= ee >>>> . >>> >>> Thank you for the information! I=E2=80=99m going to investigate this. >> [=E2=80=A6] >> >> I have written email to coletrap@uw.edu to report my findings and ask >> about details. > > Sorry, I could probably have saved you effort. I think I already mailed > before cufflinks moved to github, and I also tried to track down the > author of the problematic component, though they probably wouldn't hold > the copyright as far as I remember.. I have not received any response; neither to the bug report, nor to the email I sent. I have removed cufflinks from Guix with commit 7bf59f702. Thanks again for the report! So=E2=80=A6 I=E2=80=99ll try to see if I can adapt the GPL code from r-locf= it in a fork of Cufflinks at some point. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From unknown Sun Jun 22 11:37:29 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 28 Nov 2017 12:24:05 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator